A novel photochemical approach is presented to fabricate a silicon oxide (SiOx) layer, which we have named an “oxide nanoskin” (ONS), whose thickness is defined in the molecular-order of 1~3 nm. Through the chemisorption of a vapor phase organosilane and subsequent photooxidation using 172 nm vacuum ultraviolet (UV) light, an extremely flat SiOx layer without cracks or aggregates was formed on various polymer substrates. Owing to this ONS coating, the charge density and surface acidity of the polymer substrates became almost equal to those of a native oxide-covered Si (SiOx/Si) substrate. In addition, there was marked improvement in the durability of the hydrophilicity and in the micro-wear resistance of the polymer surfaces. Moreover, organosilane self-assembled monolayer (SAM) chemistry currently available for the treatment of inorganic glass and Si substrates could be similarly utilized. Well-ordered SAMs with a wide variety of terminal-end groups (e.g., trifluorocarbon or amino groups) could be fabricated even on inert polymer substrates, in a manner similar to their fabrication on SiOx/Si substrates. Furthermore, we demonstrated the site-selective deposition of metal oxide and metal films on polymer substrates using photolithographically micropatterned SAMs as microtemplates. Well-shaped microstructures were achieved only on the polymer substrates with the ONS layer. On the substrates without the ONS layer, pattern resolution degraded significantly and growth rate decreased, since both depended greatly on the SAM density and quality. Our ONS was very useful not only in forming highly ordered SAMs on the polymer substrates, but also in obtaining excellent pattern resolution, sufficient growth rate, and adhesion of the target materials.