Nano-scale surface structures of single crystal metal oxides, especially the perovskite oxides were examined by coaxial impact collision ion scattering spectroscopy (CAICISS) and atomic force microscopy (AFM). CAICISS measurements enabled us to determine the terminating atomic species and their arrangements of single-crystal perovskite oxide substrates and epitaxial oxide films. Through thermal-annealing of the single crystal oxide substrates, atomically flat terrace and stepped structures were developed on the surface. The atomic-scale substrate engineering made it possible to attain the novel heteroepitaxial growth such as step-decoration epitaxy resulting in the nanowire structures and diamond epitaxy on the ultrasmooth sapphire substrate. The novel application of the ultrasmooth oxide substrate to the AFM observation stage for DNA molecules was also presented.