Best Duplicate file/folder remover?

I want to be able to compare files and folders within two different directories, keep directory A accurate, remove anything in both from directory B.

each directory has 100's of folders.

Basically I'm trying to organize my ebook collection.
But I don't want to end up with tons of scattered files.
I'd like to be able to delete duplicates of files found anywhere, but only remove the dupes contained within a specific directory, and not just individual folders.

the only options the programs I've tried have are delete by date, or delete withing a folder.

Have you tried Ashisoft Duplicate Finder or Clone Tools. I've never used them (I use Araxis Merge, but only for comparing), but they seem to be capable to do what you want.