The first thing to try is Scandisk, it's built into Windows. Right click on the drive in My Computer, pick Properties then tools and then Error Checking. If you click both the Auto Fix and Scan and Fix bad clusters it should do what you need. It will take a while though so it's really an overnight job.
If that doesn't clear things up then the drive manufacturers own diagnostics may be able to help, there are links to all of them in the forum sticky.