Thermal oxidation of highly oriented pyrolytic graphite (HOPG) surface treated with an oxygen plasma was studied using scanning tunneling microscopy (STM). At the temperature of 500 degrees C, many channels were observed on the surface, however the circular pits which are fabricated by the thermal oxidation were not observed. At the temperature of 600 degrees C, the tailed pits were fabricated on the surface. Large number of pits were fabricated on the HOPG surface by the proposed technique.