Self-assembled monolayers of 2-[methoxypoly(ethyleneoxy)propyl]-trimethoxysilane (Si-PEG) reduce the nonspecific binding between silicon oxide surfaces and a variety of biomolecules. The film can be patterned by electron beam lithography at 30 nm resolution. Optimal electron beam lithography exposure conditions are 4 nC/cm at 75 keV. Exposed regions of the PEG film become negatively charged and less resistant to biomolecule binding, which leads to selective adhesion of biomolecules. The patterned film acts as a template for biomolecule attachment, while the intact PEG background is strongly resistant to nonspecific binding. Binding selectivities of up to 26: 1 were observed for patterning cowpea mosaic virus, Salmonella phage P22 tailspike protein and poly(lysine) at 30 nm linewidths. (C) 2009 American Vacuum Society. [DOI: 10.1116/1.3212899]