From MediaMonkey Wiki
MediaMonkey offers 2 ways of getting rid of duplicate tracks: by finding duplicate titles, or by finding tracks with identical audio signatures. Both methods require that you choose which track to delete since automatic deletion could result in the 'wrong' track being deleted.
In the Tree, go to the Library > Files to Edit > Duplicate Titles node. The tracklist will fill with tracks that have identical titles. Manually delete the tracks you no longer require.
In the Tree, go to the Library > Files to Edit > Duplicate Content node. You'll be prompted to analyze your library for duplicates. Once analysis is complete, click the '+' to show which tracks have duplicates. Manually delete the tracks you no longer require.
Note: You can have tracks analyzed for duplicate content when they are added to the Library. To do so, enable this option in Tools > Options > Library.