Best way is to figure out how you can do it manually and not take three months to do it. Check what photos, music, and any other favourite files you need and save to an external drive and create duplicate backups. Then delete the redundant files on your PC.
If you hadn't been so lazy in the first place this problem wouldn't have occurred, if you don't mind me saying so.
These 'duplicate files remover/finders' can create havoc as well as being useless.