5 Ways Overzealous Cleaning Can Break Windows

Chris Hoffman 29-05-2014

It’s easy to go overboard with cleaning your PC. All you really need to do is run CCleaner or the Disk Cleanup tool included in Windows to delete useless files and free up disk space once in a while. If you’re cleaning your PC in other ways, be sure you know what you’re getting into — it’s easy to break something.


Deleting Your Recovery Partition

Most computers come with a recovery partition. When you decide to reinstall Windows — or use the Refresh or Reset Your PC features on Windows 8 How To Restore, Refresh, or Reset Your Windows 8 Installation In addition to the standard System Restore feature, Windows 8 has features for "refreshing" and "resetting" your PC. Think of these as ways of quickly re-installing Windows -- either keeping your personal files or deleting... Read More — your computer copies the Windows installation files from the recovery partition instead of an external CD, DVD, or USB drive.

The recovery partition uses up several gigabytes of space on your device’s internal disk. You can delete it from a partition manager or even use the recovery drive creator tool in Windows 8 to copy your recovery partition to a USB drive and then remove it, freeing up that space.


This cleans up your drive and lets you use more of the space. However, you won’t be able to reinstall Windows or reset or refresh your PC unless you made a copy of the recovery partition. Even if you made a copy, you won’t be able to reinstall your operating system if you misplace the drive you copied the recovery files to. You’ll need an original Windows installer disc, and this won’t help you reinstall the exact OS image and drivers that came with your customized windows system.

Take Home Message: Don’t remove your recovery partition unless you’ve created a recovery USB drive or disc first. If you do, be careful not to lose your recovery media.


Corrupting Your Registry

Registry cleaners work by scanning through your registry and deleting entries they think aren’t important. For example, a registry entry created by a program you uninstalled isn’t necessary, and can be removed. The Windows registry is a massive place What Is the Windows Registry and How Do I Edit It? If you need to edit the Windows registry, making a few quick changes is easy. Let's learn how to work with the registry. Read More , containing hundreds of thousands of different registry entries, both for Windows itself and third-party programs. Many of your computer’s settings are saved here.

Cleaning your registry seems like a good idea. After all, those useless, outdated registry entries are just cluttering up the place. However, these registry entries are tiny. Even if you remove thousands of them, your computer won’t be noticeably faster Using Registry Cleaner: Does Is It Really Make a Difference? Advertisements for registry cleaners are all over the Web. There’s an entire industry out there bent on convincing inexperienced computer users that their registry needs fixing, and that, for ten easy payments of $29.95, their... Read More .

Because of the sheer amount of complexity, registry cleaners can sometimes remove important registry settings. This can prevent a program you use from working properly until you reinstall it or cause other problems in Windows.

Take Home Message: Cleaning your registry isn’t worth it Don't Believe The Hype: Registry Cleaners Don't Make Windows Faster Much advice has been given on how to keep your computer running smoothly, as well as how to fix it when it has become slow. We have even published a Windows on Speed guide, written... Read More because you could run into problems and there’s no real benefit to the cleaning. if you must clean your registry, use a more trustworthy registry cleaner like the free one built into CCleaner and skip the paid registry cleaners you see advertisements for online.



Erasing System, Program, & Setting Files

Your computer has important system, program, and user setting files scattered around its file system. Deleting any of these files can cause problems with your computer. This may be obvious to the geeks among us, but we’ve all heard stories about people who started deleting important files located in the C:\Windows directory in an attempt to clean up their computers and free up space.

Take Home Message: You shouldn’t tamper with files in the C:\Windows directory or other system files unless you’re manually removing a virus and have a good reason to delete specific files.

This doesn’t just apply to files in the standard C:\Windows and C:\Program Files directories, though. For example, many games save their game files in your Documents folder. Delete these folders in an attempt to clean up your documents folder and you’ll lose your save files and settings for those games! Other directories, like the hidden C:\ProgramData and each user’s Application Data directory also contain important settings that you’d lose if you started trying to clean these folders.



Driver Cleaning

Driver cleaner utilities can purge all bits of drivers from your computer, allowing you to reinstall the offending drivers from a clean state if you’re experiencing a driver problem. Manufacturers offer their own driver cleaners, such as the AMD Clean Uninstall Utility, which uninstalls all AMD drivers from a system. There are also third-party driver cleaners.

These driver cleaners can remove drivers you’re actually using. For example, we found stories online of people being unable to use their USB mouse and keyboard after using the AMD Clean Install Utility to delete all AMD drivers — it also wiped out their USB drivers. These people will have to restore their computers in Safe Mode, or — if that doesn’t work — maybe even reinstall Windows.

Take Home Message: Use driver cleaning tools with care. They can be helpful if a particular driver causes issues and cannot be removed otherwise, but they can also make things worse.



Drive Wiping

Tools like Darik’s Boot and Nuke (DBAN) allow you to wipe an entire hard drive How to Wipe Your Hard Drive While Leaving the OS Intact Formatting a hard drive also erases Windows. But there are methods you can use to wipe a hard drive and keep Windows intact! Read More by overwriting everything on it with garbage data. Some people prefer using a tool like this one before reinstalling Windows to ensure no deleted files can be recovered from the drive Turn Back Time: 4 Tools & Tips To Restore Deleted Files In Windows One of Windows' biggest flaws could be your rescue, should you ever accidentally delete an important file: The Windows file system does not actually delete files. Until they are overwritten, deleted files can be restored. Read More . This is only necessary on Windows 7 and earlier, as the Reset Your PC feature in Windows 8 has a drive-wiping option built in.

Take Home Message: On typical consumer PCs, wiping your drive with a tool like DBAN will erase any recovery partitions on the drive. Be careful when using drive-wiping tools!


Have you ever broken something when cleaning your PC? Leave a comment and share your cautionary tale!

Image Credit: Bawl on Flickr

Related topics: Computer Maintenance, Registry Cleaner.

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  1. Nandini Dhor
    July 2, 2019 at 1:01 pm

    Nice Information you have provide About Phone Cleaner App, Thanks for Providing us a guide about apps junk file, Cache File, keep Sharing, I shall definitely recommend it to all my friends on various online platforms.

  2. hotdoge3
    June 4, 2014 at 10:33 am

    One time a cleaner said you don't need old drivers from old updates next day not boot and PC said need old driver to use system restore so go to new

  3. Louis de M.
    June 2, 2014 at 7:43 am

    I actually had something similar happen in the past.
    system32 folder got deleted because 'it was using too much space'.
    On next reboot, we found out that Windows wouldn´t boot...

  4. wwgorman
    May 31, 2014 at 3:47 am

    Microsoft flat out does not recommend Registry cleaners. They say that they do more damage than help and as one comment says with the thousands of lines of the registry what good is cleaning a half dozen do for your computer response. The down side of and registry cleaner is your computer won't work and a re-install is required.

    • dragonmouth
      June 2, 2014 at 5:54 pm

      "as one comment says with the thousands of lines of the registry what good is cleaning a half dozen"
      You'd be surprised how many orphaned Registry keys are left behind after each program uninstall. Windows is notorious for leaving garbage behind.

      When I used to de-crapify Windows Registry there were over 4500 AOL keys in the registry and that was after I uninstalled all the AOL modules. Other undesired crapware also had thousands of keys per program. After I got rid of that junk the Registry was 25%-30% smaller and the O/S was much more stable.

      The entire idea of the Windows Registry is an abortion. Whoever came up with it should be burried neck deep in an army ant anthill.

  5. pmshah
    May 31, 2014 at 2:56 am

    One can use ccleaner for cleaning your registry without a problem whatsoever. All you need to do is allow it to create full backup file of your registry and save it. I have been using it for quite some time and have NEVER had any problems with it.

  6. John W
    May 31, 2014 at 12:53 am

    I think one of the culprits of over cleaning is the use of relatively small SSD's. I'm regularly asked how to get rid of huge chunks of Windows to release SSD space. As the price of 128 and 256Gb SSD's has dropped my usual reply these days is to buy a bigger drive and leave Windows alone. A broken registry can take days to sort out.

  7. michael clyde
    May 31, 2014 at 12:45 am

    When talking about drive wiping tools you said "... you only have to do that on Win 7 and earlier. Win 8 has a built..."
    EVERY HARD DRIVE built in the last 12-15 years (at least) has a built in disk wipe utility. Doesn't matter what O.S. you have installed. you can have no O.S. installed and still wipe your drive.

    michael clyde

  8. danny
    May 30, 2014 at 7:47 pm

    if you don't know what you are doing DON'T TOUCH IT.
    and google secure erase

  9. P Saunders
    May 30, 2014 at 6:22 pm

    Every time i've used a disk defrag tool, windows self-destructed within a week. Needless to say, no more defragging.

    • pmshah
      May 31, 2014 at 3:03 am

      You have another option for achieving the same end.

      If you have another spare hard disk available simply create a ghost image of your c: drive. Format the c : drive and then restore from the ghost image. This puts your drive through a whole lot less stress then defragmenting. BTW since the times of good old Norton Defrag - dos version - there is not a single one that is worth its salt. Not a single one of them offers write verification !

  10. Oldunshavenone
    May 30, 2014 at 6:00 pm

    I've never had to use my EASEUS Todo backup recovery function until I recently did a "cleaning" with Privazer, which was a free program recommended by a knowledgeable computer newsletter contributor whom I no longer respect as much. The cleaning program did things that messed up the functioning of programs I use regularly, and I couldn't do a successful system restore on my Win 7 x64 machine, so had to resort to my first image reinstall ever, which, I'm happy to say, worked without a hiccup. So, I can now say my image backup program works great in both backing up and recovering. And I'm back to just using CCleaner again which has always worked fine in the past.

    • pmshah
      May 31, 2014 at 3:14 am

      I totally agree with you. I have 2 drives in my system. I use BootItNG as my boot manager. Have several different operating systems installed in their own independent primary partitions. I have EasyBCD installed on all of them. I have bootable versions of memtest 86+ and Norton ghost available at boot time. I do not have hibernate option and have my pagefile.sys on a secondary volume. The imaging utility built into BootItNG is too slow for my comfort as also the images take up a lot of disk space. So every Saturday morning I create a ghost image of each of the c: drives for every windows OS installed on to the second drive. These generally compress down to about a third of the size occupied on the primary partition. The best thing about this is that every file within these ghost images are available through ghostexp.exe. BTW I also trust CCleaner explicitly. Have never had a problem.

  11. Col. Panek
    May 30, 2014 at 5:08 pm

    I made a set (5) of backup DVDs, and when I needed to use them, they wouldn't install. I downloaded Windows 7 from Microsoft's site (Digital River), and it installed and registered fine, plus it didn't have the manufacturer's legendary bloatware (their initials are h and p).

    Since then I've only used openSUSE and Mint, and all my hardware works, so haven't had a need to boot Windows. My days of registry hassles, virus cleaning, and Microsoft licenses are over. For the Windows user, Zorin, Elementary, Mint and Lubuntu will be familiar. I don't recommend Ubuntu for everyone, but maybe you're not everyone.

    • GraveDigger27
      May 30, 2014 at 8:44 pm

      On my 3-year old ASUS laptop system I was able to make multiple sets of recovery DVDs that I have used a few times. However, it's far easier to use a good disk imaging program (like the free version of Macrium Reflect) to backup the entire hard drive and restore the system to a clean setup. It's also MUCH faster (I can restore the "clean" disk image in minutes versus the hours it takes using the recovery media...) I also take the opportunity to update the operating system with the latest patches, drivers and other fixes, then make an additional disk image of that configuration to an external hard drive (so I don't have to download ALL of the updates to Windows...)

      Both my desktop and laptop systems are configured to multi-boot with Windows, Ubuntu, Linux Mint and elementary OS. I've installed lots of other Linux distros to these systems over the years, but I find that these are among my favorites. Plus, when I decided to "update" my laptop from Windows 7 to Windows 8 (and then 8.1) it was easy to do since I maintain periodic disk images "just in case..."

  12. David Shear
    May 30, 2014 at 4:36 pm

    Recovery partitions are essentially useless - why would you want to put your carefully customised, updated, full of data and extra programs system , back to how it was delivered, including piles of cr*pware?.

    Simply use a good system imager (free EASUS Todo Backup is excellent) and make reasonably frequent system images. With a USB3 backup drive, and your (big - like music/films/etc) data on a separate partition, it's fast and a doddle.

    Far superior solution

  13. Matthew
    May 30, 2014 at 11:52 am

    I forget where they did the review, but many registry cleaners will wipe hundreds, even thousands of entries from a completely fresh install.
    Trouble is, many registry cleaners go for the idea of "look how good we are, we remove more than anyone else", but to use one example, a simplistic removal of destinations not present would remove references to paths for optional features on install CD.

    Now registry COMPACTERS, can achieve useful results, they do not delete keys, but close up space left by things that do.
    Effectiveness depends on just how much addition/removal there has been.

  14. Clive R
    May 30, 2014 at 10:54 am

    it would help if windows mandated that all system processes have a simple description of what they do and what they are needed for. It can be very difficult for a lay person to find an remove any rogue processes. When I hear unattended disk activity I am always suspicious and want to be able to check exactly what is running and causing the activity

    • James
      June 17, 2014 at 2:37 am

      I couldn't agree more with you Clive!

  15. Jeffrey L
    May 30, 2014 at 9:25 am

    Google Chrome was giving me problems so I used Revo Uninstaller to really clean it out. I used one of the more thorough options and it ended up deleting Windows registry files and wouldn't boot up or even boot into Startup Repair.

    After using Hiren's boot CD, I finally got my computer running again but will probably wipe and reinstall Windows after I back up all my files.

  16. Robert S
    May 30, 2014 at 5:04 am

    Great article!

    Do not touch registry cleaners! Every one I've seen has done nothing but cause problems, removing crucial entries and mistaking used keys for unused ones and deleting them. Many times deleting even "unused" keys can slow down your computer more than just leaving them there.

    Typically files in temporary folders are safe to delete, but you still need to be cautious with this, as some installers are setup incorrectly and will install an application to your temp folder!

    • Howard B
      May 30, 2014 at 8:26 pm

      As the article says, CCleaner is not over-aggressive. In the years (I do mean *years*) I've used it, including most of its functions, I've had no problems with *any* Piriform product.

    • Jim
      May 30, 2014 at 10:56 pm


      Denigrating snarky comments side, there ARE some people who do this professionally for thousands of PCs and have a different set of rules than home/hobby use. When a product, any product, breaks enterprise-level (government, banking, retail, medical, corporate) security configurations - and the result is either preventing getting work done or opening up systems to vulnerabilities - you ban it from the environment, period.

      Some utilities may have value for some situations, especially where you're at liberty to click anything and take a personal risk to put something on a system that eats performance and need to get rid of a problem you put in there, that's your choice. Never in 25 years of work from low-level PC system bit-level guts work to diagnostic software to managing corporate systems to personal systems ever found them to improve performance. Good hardware, a good clean OS install, adequate security measures and avoiding *CLICK HERE!!!* generally preclude needing to clean up messes.

      Again, I applaud MUO for checking these tools objectively. They tested for performance improvements (not malware cleanup), found none, uncovered some risks of what may only be assumed as aggressive assumptions in 'cleanup', and reported it. Not all media or users can be as objective.

  17. Jim [PC_Evil_Genius] Aspinwall
    May 30, 2014 at 4:55 am

    As I commented on Facebook... I've had 'smart' techs use MalwareBytes on enterprise-managed systems, wiping out critical Group Policy Object regkeys, finding corporate compiled apps as 'malware', killing VPN and other secure access components. The Windows Registry is a pretty amazing, resilient, efficient hierarchical database - not just a mash of esoteric text and binary strings. If you want a stable, secure OS, there are deliberate serious tools to let that happen. The days of 'wonky' Windows 3.1 through Vista are oh-ver. If you want performance try an SSD and more RAM. Thanks for posting this!!!!

    • Buffet
      May 30, 2014 at 10:16 pm

      I have SSD's and 16G of RAM - AND Malwarebytes!
      Malwarebytes never harmed anything.
      Quit playing on faceyspace and join the living.

  18. Xiu Juan Yüan
    May 29, 2014 at 10:01 pm

    On Windows 7 I use AVG PC Tuneup 2011 without deleting system restore points, then use Windows Disk clean up. Windows 8 I use Windows Disk clean up only.

  19. likefunbutnot
    May 29, 2014 at 8:19 pm

    My personal favorite are the people who start randomly disabling Windows Services because reasons. Usually, the system will still boot in whatever misbegotten configuration, but then something completely random won't be available or won't work. Note to end users: Don't do that.

  20. Pratyush Nalam
    May 29, 2014 at 5:28 pm

    I use CCleaner for removing temporary files. Also, Glary Utilities is quite good for registry cleaning as well. And I have had bad experiences with defragmenters (I'm looking at you, Auslogics).

  21. GraveDigger27
    May 29, 2014 at 3:32 pm

    I've made my Windows-based systems unusable in the past by running an over-aggressive disk cleaner, registry clean or windows repair program. Fortunately I generally maintain disk images of my systems on external hard drives and was able to restore the damaged systems without much difficulty.

    I agree that using CCleaner and the free version of the Glary Utilities to maintain a Windows-based system can be worthwhile, but I would caution people to only run these programs with the default settings. If too many things are "cleaned" it's likely that critical files will be deleted and your system might become inoperable. Even worse, many people will not be prepared by having made backups of their systems prior to running these kinds of programs. Make sure that you backup your registry before cleaning and create a restore point before running so you can recover from an error.