A method of manufacturing a perpendicular magnetic recording medium substrate is capable of reducing the waviness of all wavelength components and a recording medium is capable of reducing contact with a magnetic head to improve the flying stability of the magnetic head. The movement-estimating unit has a nominal model setting unit in which a nominal model from the scanning vector commanding unit to the probe is set. Each trench includes a first recess having a first depth and a second recess having a second depth. From this comparison result, it is judged whether the multiplexer is at fault or the AD converter is at fault. In some embodiments, the brake mechanism includes a brake plate that is movable toward and away from a surface of the wheel hub along a direction parallel to the rotation axis of the wheel.