Not sure if anyone mentioned using a machinists surface block or other reasonably flat surface to sand the pads and rotor.
The sandpaper is placed on the surface block or flat surface and the pads are moved across the sandpaper in a figure-eight motion. The same might be done for both sides of a six-bolt rotor and one side of a centerlock rotor.
The idea is to back the sandpaper with something flat and move the part against it. Using a surface block or other flat surface and rubbing the part on the block allows more control for an even surface with minimal material removal.
I've scuffed automotive rotors and pads this way many times.
-Tim-