We report a novel patterning method for a homo-polymeric poly(3-hexylthiophene) (P3HT) nanofilm particularly capable of strong adhesion to a $SiO_2$ surface. An oxidized silicon wafer substrate was micro-contact printed with n-octadecyltrichlorosilane (OTS) monolayer, and subsequently its negative pattern was selfassembled with three different amino-functionalized alkylsilanes, (3-aminopropyl)trimethoxysilane (APS), N- (2-aminoethyl)-3-aminopropyltrimethoxy silane (EDAS), and (3-trimethoxysilylpropyl) diethylenetriamine (DETAS). Then, P3HT nanofilms were selectively grown on the aminosilane pre-patterned areas via the vapor phase polymerization method. To evaluate the adhesion, patterning, and the film itself, the PEDOT nanofilms and SAMs were investigated with a $Scotch^{(R)}$ tape test, contact angle analyzer, ATR-FT-IR, and optical and atomic force microscopes. The evaluation showed that the newly developed all bottom-up process can offer a simple and inexpensive patterning method for P3HT nanofilms robustly adhered to an oxidized Si wafer surface by the mediation of $FeCl_3$ and amino-functionalized alkylsilane SAMs.