Conductive atomic force microscope (cAFM) nanopatterning is demonstrated on epitaxial graphene on SiC (0001) under ambient conditions. Nanopatterning kinetics and chemistry suggest that ambient cAFM nanopatterning induces local oxidization with the surface, interface, and bulk layers of epitaxial graphene on SiC (0001) playing distinct roles in the depth profile of the final nanopatterned structure.