A system includes an input circuit, an analog to digital converter, first and second harmonic sensor modules, a head height control module, and a weighting function module. The input circuit receives analog signals from a read/write head. The analog to digital converter generates digital samples in response to the analog signals. The first and second harmonic sensor modules determine, from the digital samples, a first magnitude of a first frequency component and a second magnitude of a second frequency component, respectively. The head height control module estimates a height of the head over a storage medium in response to a comparison of the first magnitude and the second magnitude, and selectively adjusts the height in response to the estimated height. The weighting function module applies a time domain window function to the digital samples to create modified samples on which the first and second harmonic sensor modules operate.