Are you saying you have your media files in a folder tree, and a some subset copy of those same media files in the same folder tree?
If so, these duplicate entries are easily removed from MC's database (called the "library"). You can use the Search wizard to construct a query on Filename (path) that Starts with the path to the copy you want removed from MC's database/library. These files can then be selected and removed from MC's database (select them, and hit Delete, using the Remove from database only option).