Rid Your PC Of Outdated Bookmarks, Duplicate Files, Broken Shortcuts & Empty Folders [Windows]

Tina Sieber 06-11-2012

update bookmarksCollecting is part of human nature. Over the course of a life, we collect a lot of things. For a few decades, this has been including digital data. With every backup you make, you are not only duplicating files and folders, but you are also manifesting small errors – empty folders, duplicate files, outdated bookmarks, and broken shortcuts that don’t lead anywhere anymore. Whenever you restore your data from a backup or copy them to a new computer, you carry over those imperfections. Year after year, from one device to the next, and across operating systems.


It has become incredibly easy to migrate large amounts of data, but it’s still rather hard to maintain their integrity and keep them up to date. If you want your data to be neat, you will appreciate the selection of tools presented in this article. They can help you get rid of those duplicate, broken, and outdated items in your collected data. This will not only please your sense of order, it might also save you frustration and a tiny little bit of storage space.

Empty Folders / Directories

The average computer has thousands of folders full of data. It’s no surprise that the occasional folder is created, but never filled. A small portable app called Remove Empty Directories can help you find and delete those empty folders. A short scan of less than 40 seconds I ran on around 2,500 files, 74 directories were found to be empty.

update bookmarks

You can right-click selected folders to protect them once or delete them manually. Within Settings you can customize the behavior of Remove Empty Directories, for example by adding directories that are ignored and skipped. If you change the protection of individual folders, you have to run the scan again, before you can delete all detected empty folders automatically via the Delete folders button.

Duplicate Files

Duplicate files can take up a lot of hard drive space. Fortunately, they are easy to identify and remove. Several tools exist that can scan multiple hard drives, compare files, and eliminate any superfluous duplicates.


One such tool is Auslogics Duplicate File Finder. The interface is simplistic and after a few clicks, the program is scanning through your files. Depending on how many files you have, this can take anywhere from a few minutes to hours. My scan of 30GB worth of files took almost an hour.

duplicate files windows

The results will show groups of duplicates and you have multiple options to select and delete them. Remember that you chose how to delete files in the very beginning, before running the scan.

duplicate files windows


We have previously introduced Remove Duplicate Files & Directories with Duplicate Cleaner Read More Auslogics Duplicate File Finder in more detail Trash Your Duplicate Files with Auslogics Duplicate File Finder Read More .

We have written about several more tools to find duplicates. Take your pick:

If you have identified a duplicate folder within your backups that is not quite an exact duplicate, find out How To Merge Duplicate Files & Folders With WinMerge How To Merge Duplicate Files & Folders With WinMerge Read More .

Duplicate Folders

When you find duplicate files, you will automatically identify duplicate folders, should they exist. In case you want to search for duplicate folders rather than files, however, try V Folder Dups. Select the folder or drive to search for duplicates and go through the results after the scan has completed. All duplicates will be listed and you can choose which folder to delete directly from the results.


Rid Your PC Of Outdated Bookmarks, Duplicate Files, Broken Shortcuts & Empty Folders [Windows] V Folder Dups

Broken Shortcuts

The more often you move and sort your data, the more likely you will kill shortcuts. Whether these are shortcuts within folders or on your desktop, they can easily be fixed with Broken Shortcut Fixer. The tool will immediately fix shortcuts and allow you to investigate and delete other broken shortcuts it found, but couldn’t fix.

duplicate files windows

Outdated Bookmarks

The internet changes all the time and hence the one place that will almost certainly contain ‘bad data’ is your bookmarks. You are almost sure to find outdated bookmarks because a website changed its domain or URL structure or just doesn’t exist anymore.


A great utility to clean up your bookmarks is AM-DeadLink. It supports Internet Explorer, Firefox, Opera, Chrome, and any HTML files or URLs from text files. When you launch it, you can select a browser from a drop-down window and scan then scan its bookmarks. Once the scan has finished, you can sort bookmarks and delete outdated ones collectively.

update bookmarks

For a more in-depth review of AM-DeadLink, see the article Clean Up Your Bookmarks by Removing Dead Links And Duplicates AM-Deadlink: Clean Up Your Bookmarks by Removing Dead Links And Duplicates Read More .

If you don’t have a need for a tool that can scan bookmarks for multiple browsers because you only use Chrome, have a look at Bookmark Sentry [No Longer Available], which we have also profiled in the MakeUseOf Directory Creative Ways You Need to Try to Organize Your Bookmarks But, what really is the best way to save and organize bookmarks? Here are a few creative ways to do so, depending on your style and browser use. Read More . Bookmark Sentry checks for bad links and duplicates and can run on a schedule.

More to Clean

Are you in the cleaning mood now? MakeUseOf won’t let you down! After fixing your personal files, you can go ahead and clean Windows. Here are the articles you will want to refer to:

How do you keep your system and your backups clean and tidy? Do you have any tips or do you not feel the need at all?

Image credits: Colorful Folders via Shutterstock

Related topics: Computer Maintenance, File Management, Online Bookmarks.

Affiliate Disclosure: By buying the products we recommend, you help keep the site alive. Read more.

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  1. Jasmine
    January 20, 2016 at 2:20 am

    Deadlink is commonly known to delete links that are not actually "dead" - double check every one before it deletes!

  2. Erik
    January 30, 2013 at 4:51 am

    The problem I invariably have with duplicate file finders is deciding which file to keep and which ones to throw away. Any suggestions?

    • Tina Sieber
      January 30, 2013 at 9:53 am

      Does it matter? If the files are truly duplicates, then either copy is fine, no? Keep the one that is in the most convenient location I guess. To be honest, I'm not sure what the problem is.

      • Erik
        February 1, 2013 at 9:38 am

        I would have to disagree. I ran a search and found 37541 files on my laptop with duplicates for a total of 7.87 GB. The following example is typical for Microsoft software and is what concerns me:

        PresentationFramework.xml (3.42 MB)
        C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\

        C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\

        The same file in two different locations. Despite what you say I'm hesitant to delete either one. I don't which one (if either) I can safely delete. It's kind of like dealing with the registry -- if you don't know whether it's safe to change a key you leave it alone.

        • Tina
          February 1, 2013 at 12:26 pm


          I wouldn't touch system or program files. I guess I should not have assumed that this is common knowledge.

        • Samir
          May 31, 2016 at 9:44 am

          "The same file in two different locations. Despite what you say I’m hesitant to delete either one. I don’t which one (if either) I can safely delete. It’s kind of like dealing with the registry — if you don’t know whether it’s safe to change a key you leave it alone."

          Erik, you sound like a true nerd! That's the spirit mate! You are absolutely right in your judgment. Don't just blindly delete files because they are duplicates. If ever in doubt, use your own judgment to decide. Don't listen to what everyone else has to say, and you should absolutely not be a slave to a dumb computer program and follow its every command. You are probably smarter than the program.

          Like I said, avoid the problem of dupes by getting the discipline to store your files properly and don't leave them laying around. It's just like in a real office you know. You don't leave files and folders laying on a desk, especially if they contain top secret information. You would get fired from the job if your boss finds you doing that. As you should! What you want to do is store your files away in a file cabinet when you don't use them, and perhaps lock them down. It's the same thing with computer files and folders.

          These deduper programs are mostly geared towards computer illiterate people. It's like those dumb "optimize your PC" sort of programs. They are pretty much useless, and they are unnecessary. What people need is education and computer literacy, so that these problems don't occur in the first place, so that they can avoid using these sort of programs altogether.

    • Samir
      May 31, 2016 at 9:33 am

      I generally like to keep the ones with the older date and time stamp. If I am archiving some files, I really don't want to flip up the date and time stamps. If two files are binary identical, but one is last modified on 13 March, 1999 and another on 17 February, 2013, then I would want to keep the former. You say why? Well, why not? I don't want to lie to myself by keeping the file with the newer time stamp. If I ever want to go back to my files and see when a file was created, I of course want to see when it was created for the first time, not when it was touched or accessed last time.

      Call me insane if you want, but that's how I operate. Date and time preservation is important to me. If you are a true nerd then you will understand why these things do matter! As simple as that! Of course, the FAT and NTFS file systems don't make it simple for you to preserve this metadata. But that's another story. So if I am offered a choice, I go for the file with the older time stamp.

      I'll tell you one way this is important! Let's say you finally learn to program, and you finally get the grips on your computer and how it operates, and you finally are able to write your own program to do exactly what you want it to. You may decide to write a program that operates on your data and does something very specific with it, something that involves data and time stamps. Then you may have varying or undesired results depending on your date and time stamps.

      For instance, one thing I once did is I wrote a program that went on to look at the date and time stamps of the files on one of my disks, then created a table of dates and times. I simply wanted to figure out what my oldest stored files were. I think it was a file from 2003. If I wanted, I could have used that table to create a graphical, visual representation of the entire timeline. Sort of like Facebook timeline, but in terms of my computer addiction and file creations and mods. Now if that file from 2003 had a duplicate with a date stamp of 2007 and I got rid of the one with the date stamp of 2003, then some other file would have popped up as my oldest file, maybe a file from 2004, who knows? See what I mean now? Meta data is just as important as data itself! Just ask Google!

      Generally, you should not trust these file deduper programs. As a professional nerd, and computer addict, I can tell you, I have used a dozen of these over the years. They all had very varying level of quality, and very different results and the way they operated. If I ever again decide that I need one of these programs, I will write it myself, for my own specific use cases and criteria.

      But generally, you don't want to and you should not need to use one of these programs at all! When or if you do, then write it yourself. But if you need one, then you know you have done something wrong. What you want to be doing instead is training yourself at getting the discipline of "filing" your files where they belong when you save and create them. Don't just leave them laying around on your desktop! Get to it and store them where they should be stored. You need a folder structure hierarchy for storing your files properly. What kind of hierarchy you need it up to you to decide.

      Oh and don't just blindly delete dupes as a rule of thumb! That's the rule of dumb! There is often a very good reason why you may have two identical files in two locations. These can be system or program specific files created by the system or a program. But they might as well be your own user files. If you otherwise have the discipline of storing files properly, then you must have had an underlying thought when you chose to store the same file in two locations. Only you can know what your thought with that was. It's good to leave some clues for yourself when you do this. You can e.g. name the file a bit differently, or leave a text note.

  3. Jerry Berry
    November 29, 2012 at 10:34 pm

    Don't try quite so hard: "Simple" would do.
    (sim·plis·tic /sim?plistik/ adjective: Treating complex issues and problems as if they were much simpler than they really are: "simplistic solutions".)

  4. Edward Bellair
    November 25, 2012 at 2:21 am

    Good plan

  5. William Lundy
    November 20, 2012 at 4:50 pm

    I liked the look of AM-Deadlink and tried it out. It was very thorough and identified not only "dead" bookmarks, but redirects and allowed me to see some redundant filing I'd done. HOWEVER, when I installed it, it wanted to download a new search tool (forget the name). Even though I un-checked it (at two points in the install dialog), it still installed and set itself up as my home page in my browser (Firefox). I re-set my home page, only to find that at nest boot-up, it had again hijacked Firefox. Only when I uninstalled it (a total of 3 programs were installed as well as AM-deadlink) did it cease hijacking my browser. So, I'd recommend watching for thi and if you still download and install it, be prepared for a little extra work after the fact in dealing with this nasty little search tool.

    • Tina
      November 21, 2012 at 10:10 am


      Thank you very much for the heads-up and sorry that you had such a bad experience with AM-DeadLink!

      I still have the program installed and haven't experienced these issues at all. However, I have a routine installing stuff and may have caught a check mark you didn't.

      That said, when I do notice an unusual amount of toolbar / crapware options during installation, I usually do caution readers. If it's too bad, I don't recommend or write about the tool at all. I have to say that I don't remember anything unusual for AM-DeadLink.

      I also just noticed that there is no ling to the program in the article. Where did you download it from? Could it be that you used a third party installer? I downloaded directly from the developer:

  6. Douglas Mutay
    November 9, 2012 at 10:53 am

    Thanks for the help!

  7. Keith D.
    November 8, 2012 at 2:40 am

    Tina, this is a GREAT article. Very informative and practical. Have also greatly enjoyed reading it. Anxious for the next article!

    • Tina
      November 8, 2012 at 10:58 am

      Appreciate the feedback, Keith!

  8. Anonymous
    November 7, 2012 at 4:50 pm

    Thanks, I have been looking for a dupe file finder.

  9. Michael Jan Moratalla
    November 7, 2012 at 2:40 pm

    wow nice this is really nice

  10. Nikhil Chandak
    November 7, 2012 at 1:19 pm

    amazing tools to keep our computer clean !!

  11. Terafall
    November 7, 2012 at 10:38 am

    Thanks Tina.Now I have more space in my hard drive

  12. Lisa Santika Onggrid
    November 7, 2012 at 10:11 am

    One warning: Remove Empty Directory is not a toy. It can devastate your drive and making some apps crash if you're not careful. Sometimes the 'empty' folder is needed.

  13. Chaos Emperor
    November 7, 2012 at 9:24 am

    I will clean my computer right away

  14. ha14
    November 7, 2012 at 9:17 am

    Deleting empty folders sometime is dangerous One of the reasons is that Windows create them because they are needed during various situations, some empty folders created by drivers are important. Be sure to check before final judgement.

    • Tina
      November 7, 2012 at 3:47 pm

      Thanks for the heads-up! Wouldn't Windows just re-create the folders if it ended up needing them for some reason?

      • ha14
        November 7, 2012 at 4:42 pm

        sure Windows should recreate system empty folders upon reboot. Some software do also create empty folders if you delete them then upon reboot probably will not be recreated so if they need them they will complain. When you Uninstall programs, empty folders are sometime left behind, and these can be deleted.

  15. Norbert Gruszfeld
    November 7, 2012 at 9:16 am

    cool, Just in time for my fall computer clean up and windows reinstal

  16. Josh
    November 7, 2012 at 12:36 am

    Actually AM-Deadlink only allows you to remove old/duplicate/dead bookmarks from IE. I updated my install about two weeks ago and it would not do this for Firefox or Chrome. Anyone know why? Is there a setting that needs to be changed?

  17. john rigby
    November 6, 2012 at 11:20 pm

    Thank you TIna!
    THIS page is going to be on my Xmas "gift" list to everyone I know for their New Year Resolutions list.

    I recently found "everything" here on the Site and it is a magic PC Files Manager. Its comments were closed which prompted an idea:
    MUO staff could look backwards in all their "spare time"(???) :-) to re-open and update some of the best finds.

    • Tina
      November 7, 2012 at 3:46 pm


      Thank you for the feedback and suggestion. I am forwarding that to the team. It gives us a great boost to hear from people who enjoy reading MakeUseOf! :)

  18. Dan Worwood
    November 6, 2012 at 10:19 pm

    Thanks! About time I started cleaning my computer

  19. Steve Critchley
    November 6, 2012 at 8:01 pm

    time for a clean up