If you use the built in ripper with AnyDVD HD on Blu Ray movies, you get two choices. You can rip the entire movie to the hard drive as files, or you can rip the entire movie to the hard drive as an ISO. You do not get the choice to rip just the main movie.
It is possible to run AnyDVD HD in the background to break encryption, then use something like ClownBD to select just the main movie without extras or menus. ClownBD will only copy, not compress anything.
I prefer to rip the entire movie to the hard drive and work with it there, especially since I'm normally compressing to fit a 25gb BD disk using BDRebuilder. Working from one hard drive to a second one is much faster than working from the optical drive.
BD Rebuilder and ClownBD are free to use by the way.