This paper describes self-assembled monolayers (SAMs) that contain embedded disulfide bonds and the selective cleavage of the disulfides by electron-beam lithography (EBL). Phenyl(3-trimethoxysilylpropyl)-disulfide (1) forms siloxane SAMs with a root-mean-square roughness of 1.8 Angstrom. The disulfide bonds in I remain intact in the SAM and can react with dithiothreitol after monolayer formation, forming surface thiols, which can be derivatized with maleimide dyes. Atomic force microscopy (AFM) anodization and EBL have been used to create high-resolution patterns on the disulfide-containing monolayer. AFM anodization on monolayer I achieves 20-nm resolution lines with both topographic and chemical alterations in the patterned region. EBL with an accelerating voltage of 30 kV generates trenches 3-4 Angstrom deep and 30 nm wide. According to AFM topographic and friction images, X-ray photoelectron spectroscopy damage simulation, and chemical rebinding tests, the chemical changes induced by EBL are consistent with cleavage of the disulfide bonds to form sulfhydryl groups. The resulting chemical patterns can be further developed by reaction with N-(1-pyrene)maleimide.