IIRC, these Treks were pretty well dented to start with, so I'm not sure how much more clearance you are going to get with that approach. You can get a chainstay into most bench vises, so that's the approach I would take if I wanted it to look good. Using appropriate cauls, obviously.
See here for procedure:
http://alexandchristine.smugmug.com/...P1080110-M.jpg