A linked-crater structure was fabricated on an Al surface by chemical and electrochemical combination processes. The surface of an Al plate was treated with semiClean and was successively processed in anodization in H2SO4. Dynamic force microscopy image showed that a linked-crater structure was formed on the Al surface. The crater size ranged from 80 to 200 nm. It turned out that a lot of pores with 9 nm in diameter were created inside each crater. The depth of each crater was approximately 7–17 nm. At the next stage, the thin film growth of polythiophene on the linked-crater structured Al surface was conducted by an electrochemical synthetic method. The electrochemical polymerization on the Al surface was performed in acetonitrile containing thiophene monomer and (Et)4NBF4 as a supporting electrolyte. After being electrochemically processed, the contour image of each crater was still recognized implying that the polymer nanofilm was grown on the nanoscale structured Al surface. The cross section analysis demonstrated that the nanofilm was grown along the linked-crater structure because the contour of each crater became thick. The average thickness of the polymer film was estimated as 10–20 nm. Furthermore, copper phthalocyanine molecules were successfully injected into the polymer nanofilm on the Al surface in order to functionalize the nanoscale material.