Need assistance with erasing duplicate files

I am new to the Comodo scene and I have a questions about using System Cleaner. I know that I have a lot of duplicate files since I’ve never cleaned them out. What worries me is exactly how does one determine which one to erase and which ones not too. If someone could help me out here I would greatly appreciate it. I don’t want to mess up my system. If the program lists duplicate files can one simple clean them?