Good question. Powdercoat is really thick, particularly on the bottom bracket, where it seemed to coalesce. The shop re-faced (I think that's the correct word) them so the bearing cups and headset cups would have a flat surface to mate with once again. They had a tool that they spun by hand about the axis of the BB and of the headtube, and it sort of shaved off a thin layer.

The frame can be prepped ahead of time so this step isn't necessary (some sort of taping process), but the powdercoaters I took it to don't specialize in bicycles and apparently don't have this fine point down yet. However, a guy at the LBS knows the guy at the powdercoater and is going to teach them about prepping the frame. The result was still good; it just required an extra step.

Some powdercoaters (like Spectrum Powderworks) specialize more in bikes, and I assume they already know how to tape off these surfaces.