A read/write channel for a hard disk drive comprising at least one analog read component and a fly height control system. The fly height control system controls fly height based on a current fly height value generated based on a fly height measurement signal that passes through the at least one analog read component. The read/write channel comprises a calibration signal generator and a processor. The calibration signal generator generates a calibration signal that is coupled to the at least analog read component to place the read/write channel in a calibration mode. The processor generates compensation data based on an output of the at least one analog read component when the read/write channel is in the calibration mode. The processor generates the current fly height value based on the fly height measurement signal and the compensation data when the read/write channel is in a fly height measurement mode.