It happens from time to time that folders are not deleted when uninstalling software in Windows. It can also happen that other applications move data and leave folders intact in the process. This happend to me when I used a new mp3 tagging software that moved all my mp3 files to a new directory leaving the old folders empty.
While empty folders do not necessarily influence system performance they do influence usablity. Take a look at your ‘program files’ folder for instance. I would bet that you find several empty folders in there which are not really helpful if you are searching for a specific file in one of the program files folders.
RED, which means Remove Empty Directories, is a software that scans your hard drives and lists all empty folders that have been found in the process. All folders are displayed with their attributes which means that you can easily see root, hidden or locked folders and delete only the folders that have not a certain attribute.

I would suggest to scan specific folders only if you want to be on the safe side. It would be possible for instance to scan only the program files or my documents folders or folders on different hard drives which reduces the possibilities that you delete a folder that is required by Windows.
It is furthermore possible to create rules to keep or delete folders and ignore empty files in folders.
Read More:
Remove Empty Directories
via Download Squad
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[...] start menu. An easy way to delete empty folders in the Windows Start Menu is to use a program like Remove Empty Directories and point it to the path on the computer system that stores the start menu entries (Documents and [...]
[...] Otra alternativa, que no he probado personalmente, es el Remove Empty Directories (via ghacks): [...]