HI Bass,
well this isthe way I do what your asking about, but FIRST backup your website somewhere safe.
If you have NOT moved any of the images or files used from the original location when you made your website, then this could work or you'll have to hunt down where they are.
First open VSD and then minimize it. Now go to "My Documents" (or where ever your website folder is)
and open that. If your just wanting to clean the files folder open that folder. select all and delete.....yes delete.
Now minimize the files folder and maximize VSD. Click save and check your files folder out. If nothing has been moved as previously stated, all should be good. If you have moved some items then when you preview your website it will ask you for the location of what is missing.
my example is a theme with just a few pages. remember coffeecup is NOT responsible if you decide to use this suggestion.
http://www.myofficialnewbie.com/tutorials/clearingwebsitefolder.html