How to Solve Duplicate File Problem on iTunes

I find that I have three or four copies show up in my itunes folder for just about every album I have. Itransferred all my CDs to itunes (Apple Lossless format) a couple of years ago. The only exceptions are recent files I added (new CDs). Is there a way to remove these duplicate references? I'm not sure why they're showing up. I have had one or two harddrive fails, and I created a backup directory for music at one point, which have have had something to do with it - but it should be a backup, not a duplicate.

Any help would be apprecaited in knowing how to remove these dupes, and on keeping proper backup going forwrd.

Am using a PC, iTunes, all Apple Lossless files. Am also open to changing to another interface as long as it's convenient. I do like the itunes remote access via iphone though..