Remove Duplicate Music Files, But Keep iTunes Copy

How can you remove duplicate copies of music files on your hard drive but be sure to keep the one iTunes is using and keeping the iTunes Library intact?
I have hundred of duplicate music files, using a tool like CleanGenius or others I can get a list of duplicate files, but I do not want to break iTunes Library and only want to remove the duplicates that are not being used in iTunes.

I have the same issue. If I have a file in my music folder and then click on it and it opens in itunes it creates a duplicate file in my itunes library. Besides sorting in finder and deleting one by one based upon folder location is there a less mind numbing way to accomplish this task.
Or do I have to pay the $10 for a program like Gemini?

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