We report a systematic modification of thin YBa 2 Cu 3 O y films with a scanning tunneling microscope. The samples include YBa 2 Cu 3 O y films on MgO(001) and YBa 2 Cu 3 O y /PrBa 2 Cu 3 O y bilayer films on SrTiO 3 (001). The bias voltage of the tip was kept negative and varied from -600 to -1200 mV. The tip was operated in a constant tunneling current mode with tunneling current 0.3-0.7 nA and scanning rate 1 Hz. Modification of the surface begins with nucleation of holes, or at the edge of a dislocation or protrusion on the surface, and is achieved by successively scanning a fixed area. We show the image obtained from an atomic force microscope which can help us look into the mechanism of the modification.