Use bondo body filler. I think you can find it at walmart or an auto parts store. Just fill it in, let it harden, and then sand it down, and repaint it. You need to put it on a lot of space, not just on the holes so it looks legit. Here is a video that shows this being applied to a roof rack holes.
Just wait until 0:28 to see the bondo, and to see it applied to the model.
http://www.youtube.com/watch?v=V_-ebjzni-o
