We report the results of a study into the factors controlling the quality of nanolithographic imaging. Self-assembled monolayer SAM coverage, subsequent postetch pattern definition, and minimum feature size all depend on the quality of the Au substrate used in material mask atomic nanolithographic experiments. We find that sputtered Au substrates yield much smoother surfaces and a higher density of 111-oriented grains than evaporated Au surfaces. Phase imaging with an atomic force microscope shows that the quality and percentage coverage of SAM adsorption are much greater for sputtered Au surfaces. Exposure of the self-assembled monolayer to an optically cooled atomic Cs beam traversing a two-dimensional array of submicron material masks mounted a few microns above the self-assembled monolayer surface allowed determination of the minimum average Cs dose 2 Cs atoms per self-assembled monolayer molecule to write the monolayer. Suitable wet etching, with etch rates of 2.2 nm min −1 , results in optimized pattern definition. Utilizing these optimizations, material mask features as small as 230 nm in diameter with a fractional depth gradient of 0.8/ 20 nm were realized. © 2005 American Institute of Physics.