Anodic oxidation via atomic force microscopy is a promising method for creating submicron-sized silicon dioxide patterns on a local surface. The area patterned by AFM anodic oxidation (AAO) has different chemical properties from the non-patterned area, and thus site-selective modification of patterned surfaces is quite possible. In this study, we combined the AAO with self-assembly method and/or wet chemical etching method for the fabrication of positive and/or negative structures. These locally modified surfaces could be used to the site-selective arrangement and integration of various materials based on a pre-described pattern.