Rid Your PC Of Outdated Bookmarks, Duplicate Files, Broken Shortcuts & Empty Folders [Windows]

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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are not only duplicating files and folders, but you are also manifesting small errors – empty folders, duplicate files, outdated bookmarks, and broken shortcuts that don’t lead anywhere anymore.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 They can help you get rid of those duplicate, broken, and outdated items in your collected data.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.

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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 Auslogics Duplicate File Finder in more detail.

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.

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.

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.

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, which we have also profiled in the MakeUseOf Directory. 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

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26 Comments - Write a Comment


Steve Critchley

time for a clean up


Dan Worwood

Thanks! About time I started cleaning my computer


john rigby

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.



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! :)



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?


Norbert Gruszfeld

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



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.


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


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.


Chaos Emperor

I will clean my computer right away


Lisa Santika Onggrid

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.



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


Nikhil Chandak

amazing tools to keep our computer clean !!


Michael Jan Moratalla

wow nice this is really nice



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


Keith D.

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


Appreciate the feedback, Keith!


Douglas Mutay

Thanks for the help!


William Lundy

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.



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: http://www.aignes.com/deadlink.htm


Edward Bellair

Good plan


Jerry Berry

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”.)



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

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.


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.



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

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