Electron and ion beam lithographic techniques were used to pattern self-assembled monolayers with organic functional groups. Nucleation and growth of minerals from aqueous solution were confined to the patterned regions. A vinyl-terminated self-assembled monolayer (SAM) was selectively deposited in ion and electron beam etched regions of a methyl-terminated SAM. Sulfonation of the vinyl groups produced a surface patterned in either hydrophobic methyl groups or hydrophilic sulfonate groups. Subsequent growth of FeOOH films was confined to the sulfonated regions. Condensation images were used to image each step in the lithographic scheme. Resolution of the SAM patterning step was 1-3 mum, while resolution of the mineral deposition step was 10-15 mum.