An electron beam writing system includes an electron beam patterning machine operable to emit an electron beam to form a pattern on a substrate. A computer control system, coupled to the electron beam patterning machine, has a plurality of pre-computed distortion maps. Each distortion map describes expected distortions of the substrate caused by bulk heating resulting from exposure to the electron beam. The computer control system controls the electron beam patterning machine using the distortion maps in order to adjust for the expected distortions.