Self-assembled monolayers (SAMs) formed from alkanethiols on thin films of gold were exposed to abeam of metastable argon atoms through a stencil mask. The changes in the organizational structure ofthe alkyl chains in the SAM that resulted from exposure were characterized using reflection−absorptioninfrared spectroscopy. All spectroscopic evidence suggested that the SAMs become disordered after exposureto metastable argon atoms and that no apparent oxidation of the alkane chain occurred. The alkanethiolatesin the regions of a SAM of dodecanethiolate damaged by the atom beam exchanged readily upon immersionin a solution of 16-mercaptohexadecanoic acid. The exchange reaction was selective for the regions of theSAM exposed to metastable argon atoms with patterns containing critical dimensions of <50 nm. A thin(<5 nm) polymeric multilayer was covalently linked to the carboxylic acid groups in the exposed regionsof the SAM. The polymeric layer served as an improved resist against a commercial KI/I2-based etchantused to transfer the pattern into the thin film of gold.