I've been using MS Word when I can to cleanup, and then exporting to HTML or RTF and converting from there.
Word has a simple search and replace syntax(although you can do regex if you like) so you can say something like "[File:*2007]" and replace it with nothing, which is a lot easier then regex IMO. That said, if you were doing something more complex RegEx would definately be the way to go, it just takes me 20 minutes to get a regex for something simple even right.