Systematic modifications on the nanometer scale of YBa2Cu3O7-delta (YBCO) epitaxial, thin films have been achieved by using a scanning tunneling microscope in air at room temperature. Working with tunneling parameters slightly above those used for imaging results in irreversible, nanometer-sized surface modifications. The surface topography of our YBCO films showed characteristic growth spirals, of which one revealed a remarkable ''S''-shaped top end. This unusual growth behavior indicates possibly a distortion caused by a line defect in the second to last turn of the spiral. We succeeded in cutting through this structure by producing a 2.5 nm wide groove across it. This corresponds to the controlled removal of only a few unit cells of YBCO. As an alternative modification technique, bias voltage pulses were applied, leading to the formation of 3 nm wide craters. (C) 1996 American Institute of Physics.