In order to get atomic smooth rigid disk substrate surface, ultra-fined alumina slurry and nanometer silica slurry are prepared, and two steps chemical-mechanical polishing (CMP) of rigid disk substrate in the two slurries are studied. The results show that, during the first step CMP in the alumina slurry, a high material removal rate is reached, and the average roughness (Ra) and the average waviness (Wa) of the polished surfaces can be decreased from previous 1.4 nm and 1.6 nm to about 0.6 nm and 0.7 nm, respectively. By using the nanometer silica slurry and optimized polishing process parameters in the second step CMP, the Ra and the Wa of the polished surfaces can be further reduced to 0.038 nm and 0.06 nm, respectively. Atom force microscopy (AFM) analysis shows that the final polished surfaces are ultra-smooth without micro-defects.