Yes...I "scalped" my Tahoe about a year ago. After removal of the racks which was straight forward and easy, I: 1) used allen head threaded inserts to fill the existing bolt holes, 2) painted the insert heads black to match paint...and 3) topped off with a thin coat of clear silicon sealer.
Gave it a cleaner look, but rack mounts to roof left areas that needed to be buffed out. I tried not to use anything too abrasive shy of rubbing compound, but still could not manage to pull out the outline of the rack mounts. Took to local detailer to see what it would run and he quoted me $150 to color sand out. For $150, I'll hold out - after all, it is on the roof! Still bugs me know it is there. Good luck and let me know how it goes! Anyone else have any ideas for pulling out the rack mount marks?