A Windows only program, RED is a nifty little utility for deleting empty directories in your Windows system. RED stands for Remove Empty directories and helps you in batch deleting folders which are empty.
Just point RED at the drive you want to clean up. RED scans and gives you a list of all empty folders in that drive. You can target a folder too. Then hit the button “Delete All” to get rid of those folders. Or if you want you can selectively delete folders.
I found this program to be very useful when I had auto-organized by music files which left behind a lot of empty folders. 
Download Remove Empty Directories
P.S. - Do not run this on system drives. You may run into problems.
Good thing that you warned not to run it in system drives. But I wonder, how many empty folders are there in C:\ ?
I must say lots …
I have 397 empty folders in C: 
But I don’t think I should try the risk of deleting those.
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Cheers! Sandra. R.
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