A %20 is a url-speak for a space. But it's quite uncommon to see those on the c-drive.
So now my questions:
1. Do you have the 'nornal' Documents and Settings and Program Files folders also?
2. What do you mean with "microsoft visio files"?
3. What do you mean with "compilation of my Java program" and how do you know it's caused by these folders?
4. What problem is created if you delete these folders?