Kevin,
The examples that Karl and Cecilia gave were taken from the floorplan in 2d only. The problem that ArthurG and Bier are having is that this clean-up does not occur in 3d as well (which it probably should, i.e. it's a bug/shortcoming).
Firstly, check you definitely have 'enable skin priorities' ticked in the walls settings, and that the walls are all on the same layer (or if on different layers, make sure they have the same layer intersection number), and that you have 'Clean Wall/Beam Intersections' turned on in the On-screen View Options (found on the 'View' menu, or the OSVO toolbar).
If you then follow Cecilias advice concerning the skin priorities, then it should work fine in 2d.
Archiben posted a very useful guide to what priority to give each kind of skin, which I follow religiously and works for almost every occasion -
http://archicad-talk.graphisoft.com/viewtopic.php?t=14758.
Please post a screenshot if you are still having problems.