In this study, in order to investigate how consecutive treatments of glass surface with HF acid and water vapor/Ar plasma affect the quality of 3-aminopropyltriethoxysilane self-assembled monolayer (APS-SAM), poly(3,4-ethylenedioxythiophene) (PEDOT) thin films were vapor phase-polymerized immediately after spin coating of FeCl3 and poly-urethane diol-mixed oxidant solution on the monolayer surfaces prepared at various treatment conditions. For the film characterization, various poweful tools were used, e.g., FE-SEM, an optical microscope, four point probe, and a contact angle analyzer. The characterization revealed that HF treatment is not desirable for the synthesis of a high quality PEDOT thin film via vapor phase polymerization method. Rather, sole treatment with plasma noticeably improved the quality of APS-SAM on glass surface. As a result, a highly dense and smooth PEDOT thin film was grown on uniform oxidant film-coated APS monolayer surface.