Patterning of self-assembled monolayer (SAM) was demonstrated by area-selective deposition of SAMs on a pattern made by synchrotron radiation (SR) stimulated etching SiO2 thin films. The etching was conducted by exposing the SiO2 films to SR through a Co contact mask with SF6+O2 as the reaction gas. A dodecene SAM was deposited on the etched surface and an octadecyltrichlorosilane SAM was deposited on the SiO2 surface. The deposited SAMs were densely packed and well ordered, which were characterized by infrared spectroscopy, ellipsometer, and water contact angle.