Embodiments in accordance with the present invention relate to detecting a micro-relief that exists on surfaces of a magnetic disk. A phase or frequency of a read signal obtained when data written to a minute projection or a minute concavity on a recording surface of a magnetic disk is read out, differs from that of a read signal obtained when data written to a flat recording surface is read out. The phase progresses in the minute projection, whereas the phase is delayed in the minute concavity. A micro-relief is detected by measuring a deviation value of this frequency, and then defect registration is performed. Embodiments in accordance with the present invention are configured to detect a minute projection whose level does not cause TA. Embodiments in accordance with the present invention may also be configured to provide a highly reliable magnetic disk drive by controlling the flying height in response to a state of a minute projection and that of a minute concavity.