To improve the patternability and adhesion of poly(3,4-ethylenedioxythiophene) (PEDOT) nanofilm to an SiO2 surface, an oxidized silicon wafer substrate was microcontact printed with an octadecyltrichlorosilane (OTS) monolayer, and subsequently its negative pattern was self-assembled with (3-aminopropyl)trimethoxysilane (APS) molecules. Then, a PEDOT nanofilm was selectively grown on the APS monolayer patterned area via the vapor phase polymerization (VPP) method. To evaluate the adhesion and patterning, the PEDOT nanofilm and mixed monolayer were investigated with a Scotch((R)) tape peel test, Fourier transform infrared (FT-IR) microspectrometer, X-ray photoelectron spectrometer, and optical and atomic force microscopes. The evaluation revealed that the newly developed bottom-up process can offer a robustly adhered, and selectively patterned PEDOT nanofilm on an oxidized Si wafer surface, most likely through extensive but intermittent chemical bonds between the polymer and the APS monolayer.