A beam focusing technique is developed for electron beam lithography on transparent substrates wherein the substrate height is estimated as a plane calculated from height data measured from perimeter metal. The effectiveness of this method, which avoids problems associated with metal-on-resist coatings, is verified with pores and gratings in ZEP520A resist on 1x1 in.(2) indium tin oxide/quartz slides and on 4 in. quartz wafers. Using a Vistec EBPG-5000 electron beam lithography tool at 50 keV, we achieved consistent 18 nm diameter pores at 59 nm pitch across 41 mu m of substrate tilt without direct height measurements at the writing sites.