Selective vapor deposition of conductive poly(3,4-ethylenedioxythiophene) (PEDOT), thin films has been carried out on self assembled monolayers patterned oxide substrate. Since the 3,4-ethylenedioxythiophene(EDOT) monomer can be polymerized only in the presence of oxidant such as $FeCl_3$, the PEDOT thin film is selectively deposited on patterned $FeCl_3$, which only adsorbs on the partly removed SAMs region due to the inability of $FeCl_3$ to adsorb on SAMs. Therefore, the partly removed SAMs can act as an adsorption layer for the $FeCl_3$ and also as a glue layer for the deposition of PEDOT, resulting in the significantly increased adhesion of PEDOT to $SiO_2$ substrate. The use of UV lithography and Cr patterned quartz mask provided the formation of SAMs patterns on oxide substrates, which allowed for the selective deposition of conductive PEDOT thin films.$^{oo}The$ new process was successfully developed for the selective deposition of PEDOT thin films on SAMs patterned oxide substrate, providing a new way for the patterning of vapor phase deposition of PEDOT thin films with accurate alignment and addressing the inherent adhesion issues between PEDOT and dielectrics.