You will need to look for custom covers. The back corners of the rack by the hatch area look the most unsightly without the roof rack there anymore. This thread will help, and has pictures:
http://forums.genvibe.com/zerothread?id=40461EDIT: You will also need to order new plastic clips once you remove your rails. There hasn't been anybody (to my knowledge) that has been able to remove them without busting the clips underneath. And as I understand the installation process of new caps, you will need the clips again. Here's a great write up Sheldon (scherry2) did for us a awhile back:
http://home.comcast.net/~sandk...s.htm
Steelies to the rescue.