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Sounds like all you need to do is take a grinder and cut them off, them grind them smooth.
Not quite that simple. The whole seam along the roof needs to be welded up. I did mine. Its a bit of a pain. I haven't finished fileing the welds and making it look straight but here is a few pics.
I think there's a little more to it than just snipping them off, throwing some mud on it, and painting. Like two metal sheets that would need to be re-welded.
See if I can get Rich to take pics. Experimented with it when I was about 17(oh god, that's about 10 years ago !), and it is a little tricky. But no rain when it pours. We we also shaving the drip rails on our fastback.
I started doing that to my 65 coupe a while back and have yet to finish. It's not aas simple as it may sound. Like someone said earlier the roof has to be re-welded where the rail is cut. Will try to get some pictures later tonight.