Nanostructures of poly(3,4-ethylenedioxythiophene) (PEDOT) are assembled by using an anodic aluminum oxide template directly fabricated on gold-coated silicon wafers. Inside these templates, PEDOT and hydroxy functionalized PEDOT form tubes. On the other hand, alkyl- and perfluoro-functionalized PEDOTs assembled as nanorods. This approach allows a platform to understand the molecular and nanostructural effect on the surface wettability of these materials. In the water/air interface, the contact angle of water droplet (CAwater) for the smooth alkyl-functionalized PEDOT films increases when alkyl chain gets longer. In contrast, the contact angle reachs saturation at 130° with alkyl chain longer than ethyl in assembled nanorod arrays. It remains the same even in the case of perfluoro-functionalized PEDOT. Moreover, ethyl-functionalized PEDOT (PEDOT-C2) nanorods displays superoleophilicity and the oil deoplet cannot stay on the film in water. Based on the wettability studies, it is concluded that the nanostructures contribute predominantly for the surface wettability of these nanomaterials when the length of alkyl chain crosses certain threshold.