We have systematically studied the growth mechanism and surface topography of YBa2Cu3O7-δ (YBCO) and Bi2Sr2Ca0Cu1Oy‐2201 (BSCCO) epitaxial grown superconducting films by scanning tunneling microscopy. Here we report two growth mechanisms of screw dislocation growth and layered growth; the surface characterization; and surface modification of thin films under a controlled manner. Excimer laser ablation technique was applied to synthesize high‐quality epitaxial thin films. YBCO thin films were epitaxially grown with c axis perpendicular to the SrTiO3 (100) substrate surface. If the YBCO films were grown on the substrate which normal is slightly off the ideal  orientation, the films show layered growth. Whereas on the flat substrate, the films were nucleated and grown with the screw dislocation manner. By using the effect of field‐induced evaporation, we were able to analyze the initial stage of growth. Epitaxial grown BSCCO‐2201 films on ZrO2 substrates were synthesized and studied by scanning tunneling microscopy (STM). Layered growth and larger atomic flat areas were observed, which are more stable under STM than YBCO films. No screw dislocations were identified in BSCCO‐2201 films. The reasons of the different behaviors of the two kinds of thin films are discussed.