Until you fully understand how Lightroom operates it probably isn't a good idea to try to clean up your hard drive outside of Lightroom. The Lightroom catalog is a database that keeps track of where images were when they were imported or where they were located on your hard drive. I suspect you are getting messages that your photos are missing. Here are instructions that should help you resolve the problem:
Lightroom thinks my photos are missing - how do I fix it? | The Lightroom Queen