Patterning SiO2 thin film on the Si(100) surface was successfully demonstrated using a synchrotron radiation (SR) stimulated etching technique with SR6 + O-2 as the reaction gas and a Co contact mask. The etching stopped completely at the SiO2/Si(100) interface. After the complete removal of SiO2 by SR etching, the Si surface was flat (Ra = 0.1 nm) and a well-ordered self-assembled monolayer (SAM) of dodecene was deposited on the SR etched region area selectively. Co was found to show sufficient resistivity against the SR etching and to be easily removed by dilute (similar to 0.01 N) HNO3, without damaging the SAM. The SR etching of the SiO2 thin films on the Si surface with the Co contact mask was found to be a suitable patterning technique for the area-selective deposition of alkyl SAMs. (C) 2003 American Vacuum Society. [DOI: 10.1116/1.1563256].