Vapor phase polymerization of a conductive polymer on a SiO2 surface can offer an easy and convenient means to depositing pure and conductive polymer thin films. However, the vapor phase deposition is generally associated with very poor adhesion as well as difficulty when patterning the polymer thin film onto an oxide dielectric substrate. For a significant improvement of the patternability and adhesion of Poly(3-hexylthiophene) (P3HT) thin film to a SiO2 surface, the substrate was pre-patterned with noctadecyltrichlorosilane (OTS) molecules using a μ-contact printing method. The negative patterns were then backfilled with each of three amino-functionalized silane self-assembled monolayers (SAMs) of (3-aminopropyl) trimethoxysilane (APS), N-(2-aminoethyl)-aminopropyltrimethoxysilane (EDA), and (3-trimethoxysilylpropyl)diethylenetriamine (DET). The quality and electrical properties of the patterned P3HT thin films were investigated with optical and atomic force microscopy and a four-point probe. The results exhibited excellent selective deposition and significantly improved adhesion of P3HT films to a SiO2 surface. In addition, the conductivity of polymeric thin films was relatively high (~13.51 S/cm).