The only way I know of how to do this is to group up what you have already mapped the way you want and map it accordingly. Let's say the G's are the good-mapped area of a simple terrain-like MDL file and the B's are the bad areas you want to dump entirely.
Code:
GGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGGGGGGGGGG
GGGGGGGBBBBBBGGGGGGG
GGGGGGBBBBBBBBGGGGGG
GGGGGGBBBBBBBBGGGGGG
GGGGGGGBBBBBBGGGGGGG
GGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGGGGGGGGGG
Just select everything marked as a G in this example leaving out those marked with a B. You have to be in face mode for this to work. Then go to edit > create group. Switch to group mode and select the area that isn't part of the group you created and bring up the skin edittor. Now you won't see anything in there.
This is the best method I can think of.