A hard disk drive that determines a flying height from a ratio of a first harmonic transfer function and a third harmonic transfer function. The transfer functions can be determined from a response to an impulse function. The impulse function (also known as an impulse response) can be a playback waveform de-convolved by channel data sequence. Any change in the ratio of the first and third harmonic transfer functions corresponds to a change in the flying height. The disk drive may utilize the transfer function ratios in a feedback routine to control the flying height.