The video below explains the folder flattener.

The folder flattener is a way to simplify your music organizing! 

The folder flattener is an easy-to use program that makes it possible for you reduce any number of folders into just 1. No more wasting hard drive space with unnecessary subfolders, or struggling through ITunes' complicated interface--the tool does everything automatically by itself while still allowing total control over what gets where when.

The folder flattener will consolidate all of your music folders into one. There is even a handy review folder that is added that will capture many duplicate files with the same file name. Go through this folder to ensure they are all indeed duplicates, then you can simply delete them.