If the only problem is duplicate tracks in iTunes, then you can use the iTunes built-in “Find Duplicates” feature to find and remove the duplicate tracks. This solution also requires that your tracks are properly named and have correct ID3 tags set. There are also scripts on many website to perform this, but unfortunately they can not remove the duplicate files on your hard drive. If the files on the hard drive are duplicated because of different folder/file names, then the solution is tedious and requires lots of disk space and time.
If this is the case Audio Dedupe is the tool that will save you days of work by finding duplicate audio files on your entire computer. Audio Dedupe will not only remove the duplicate files from iTunes, but it will put in order your entire audio collection.
Audio Dedupe can recognize duplicate audio files even if they are not marked with ID3tags and are stored in different file formats. This is not just a standard duplicate file finder as Audio Dedupe will actually listen to the music files and recognize if the song is the same as the others stored in different formats. It can check MP3, MP2, MP1, MPA, WAV, OGG, AIFF, AAC, MP4, FLAC, AC3, WavPack (WV), Musepack (MPC) and Windows Media Audio (WMA) file formats and allows you to clean up the duplicates to save valuable drive space.
Once you add the folders to be scanned you can choose the similarity percentage in order to narrow or broaden your search results and start the scan. In the folders panel you can also exclude some folders from the auto-check feature. This is handy if you would like to preserve the files in some "'source"' folder(s).
Audio Dedupe will put in order not only your iTunes playlist, but your entire music collection.