You could probably find some rubber or silicone plugs to fit the holes at a local auto parts store like Pep Boys. The only other option would be to have the holes welded up and repaint the top.

__________________
'05 X3 3.0i Alpine White/Gray Leather/Alum. Trim
Sport/Steptronic/Servotronic/Panoramic
Prem. Sound/Staggered 18" Style 114 Y-Spokes