If you want to charge through wood or a desk or whatever, you're probably better off with a qi setup than magsafe. They sell under desk qi wireless kits - with tuneable strength to optimize charging. IKEA also sell a relatively inexpensive one but it's pretty basic - Smojarke.

If you're set on magsafe though, best performance would probably be from routing a pocket for the magsafe charging end, and covering that over with a thin veneer. Or routing it out from the other side, so the top surface is thin, then installing the magsafe and packing it the hollow at the bottom so it's sturdy.