We use an atomic force microscope (AFM) to manipulate graphene films on a nanoscopic length scale. By means of local anodic oxidation with an AFM we are able to structure isolating trenches into single-layer and few-layer graphene flakes, opening the possibility of tabletop graphene based device fabrication. Trench sizes of less than 30 nm in width are attainable with this technique. Besides oxidation we also show the influence of mechanical peeling and scratching with an AFM of few layer graphene sheets placed on different substrates.