The creation of geometrically well-defined submicron structures on insulating substrates by e-beam lithography is hampered by surface charging. This problem becomes crucial when trying to create nanosized protein patterns by selective molecular assembly patterning (SMAP) on transparent glass substrates. In this paper we demonstrate that the use of thin films of conductive indium tin oxide resolves the issue of surface charging during e-beam writing while being compatible with the standard SMAP protocol for surface modification. © 2005 IOP Publishing Ltd.