We report the use of metastable Ar(P-3(0,2)) atoms and a physical mask to pattern octadecylsiloxane self-assembled monolayers grown directly on silicon surfaces. The damage to the monolayer is confirmed using lateral force microscopy, changes in hydrophilicity, and x-ray photoelectron spectroscopy analysis. Metastable atom exposures sufficient to uniformly damage the monolayer should allow pattern transfer to the underlying Si(100) substrate following chemical and plasma etching. With optical manipulation of the incident metastable atoms, this technique could provide the basis for massively parallel nanoscale fabrication on silicon.