Firstly, in order to check the noise level of a device, DC erasure is applied to a magnetic recording medium and the magnetic recording medium is read. Then, a test signal including a first order component and a third order harmonic frequency is written into the magnetic recording medium. The written test signal is read and Fourier transform is applied to the read signal to obtain the respective amplitude of the first order and third order harmonic components. Then, it is determined whether the amplitude of the third order harmonic component is sufficiently large compared with the obtained noise level. If the amplitude is sufficiently large, the flying height of the head is estimated using both the first order and third order harmonic components. If the amplitude is not sufficiently large, the flying height of the head is estimated using only the first order component.