A screw extractor, (EZ Out) may be your only option, unless you drill them out.
You can buy them individually, instead of buying a set. Get plastic caps from any auto parts store.
Duplicolor spray paint to match. Make sure to use sealant, preferably silicone.
Check message board or projects sections, many have removed the roof racks. Good Luck.
P.S.- Check (Fast Eddie'04) library. He has some nice pics.
Very clean, yet simple project. (As long as you can remove the rack)