A system for determining a fly height includes a first head of a disk drive, a second head of the disk drive, a capacitive sensor circuit coupled to the first head and the second head, and a logic device coupled to the capacitive sensor circuit. The capacitive sensor circuit is configured to measure a first capacitance between the first head and the first disk, remove noise from the first capacitance using a second capacitance between the second head and the second disk, and based thereon determine a corrected first capacitance. The logic device is configured to determine the fly height between the first head and the first disk using the corrected first capacitance.