We demonstrate that local oxidation using a conductive atomic force microscope (c-AFM) can achieve patterning of sub-10-nm spots on protein-resistant oligo(ethylene glycol)-terminated alkyl monolayers on silicon substrates. Such a high resolution of nanopatterning with a c-AFM on organic thin films was realized for the first time by applying ultrashort (50-100 ns) voltage pulses to the silicon substrate relative to the conducting AFM tip. Furthermore, the nanopatterning can be controlled at the surface of the hydrophilic monolayer without oxidizing the silicon interface.