Systematic modifications on the nanometer scale of YBa2Cu3O7−&dgr;(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. ©1996 American Institute of Physics.