I believe you're talking about shaving off the drip rails.
I've done this, its not that hard, just need to be careful when you're doing this.
Once you pull the trim, you'll see the pinch weld where the roof is welded up. You'll need to cut off this pinch weld, and weld up the resulting gap.
Go slow, taking just a couple of inches at time. Its very easy to get a wavy line, so just keep an overall eye on the curvature of the edge that you're in the process of making. Even so expect to do some rework on this line after you're done. The roof at this area pretty tolerant (in my opinion), so you don't need to be super careful about the heat you're putting into it (but don't go nuts, still treat it like any other piece of ~20 gauge sheet metal).
If you're going to do this, and paint the car, I would highly suggest you add the doubler panels to the the top and bottom of the windshield corners, and the over the Y-Joint at the end of the cabin/roof/quarter panel interface. This should help to prevent any stress cracks from appearing in you're new paint in the future.
...and be prepared to remove a lot of lead from all these areas.
Hope that helps some,
Dave