In this paper, the Cu(001) surface covered with glycylglycine has been studied by scanning tunneling microscope(STM) under ultra_high vacuum condition. On that surface copper clusters in nanometer_scale, which could form alphabet or graph a t our wishes, may be produced by the scanning of STM under a certain bias voltag e condition. The height of these clusters has a close relation with bias voltage , tunnel current and time. It offers the opportunity to fabricate nanometer_scal e apparatus by these clusters due to their stability at room temperature. The ex perimental result shows that the copper atoms which form these clusters come fro m neither copper substrate surface nor STM tip. We think that the tensile stress field in the copper substrate is produced due to the chemisorbed glycylglycine molecule in tunnel electric field and it is the migration of copper subsurface i nterstitial atoms under that tensile stress field that causes the formation of c opper clusters.