Download a program called Lupas Rename or else an alternative is a program called R-Name It. These are VERY POWERFUL batch renaming programs where you could for example select all your filenames and replace all SPACES with anythink (like underscores for exampel) or you could remove all [!]'s.
By the way, it sounds like all your roms (or some of them) have been renamed using GoodTools. These are basically rom organizers where you can rename roms however you want. But if I were you, I'd recommend going with the batch renaming programs.