An indentation is formed by thrusting a probe of a scanning probe microscope for processing, which has a vertical surface or a vertical ridge and is harder than sample material, into sample for measuring the indentation. A high-fidelity AFM observation is performed on the shape of the formed indentation with a thin probe with high aspect ratio, the direction of the vertical surface or the vertical ridge is inspected, and the angle error .theta. is stored. By rotating a sample stage by an angle corresponding to the measured mounting angle error .theta. of the probe, the mounting angle error of the probe is corrected in advance.