Roughness parameters such as the root-mean-square (RMS) roughness in super smooth surfaces are heavily influenced by evaluation ways and measuring method. With the help of CCI6000, relationships were investigated respectively between the RMS roughness with the instrument parameter set and cutoff wavelength. The study revealed that there was an optimal set of measurement parameters and a dynamic cutoff wavelength that would identify different wavelength regimes when measuring super smooth surfaces. It was found that the proposed scheme greatly reduced the influences of CCI instrument parameters and cutoff length on RMS roughness in the measurement of hard disk surfaces. RMS roughness exhibited a steady-state trend and the processed surface morphology conformed to the arrangement of atoms and the polishing feature of CMP technique.