A disk drive is disclosed operable to seek a head from a first radial location over a disk to a second radial location over the disk. A reference signal is initialized, a feed-forward control signal is initialized, and a seek is initiated. During the seek operation, a position error signal (PES) is generated and saved, wherein the PES represents a position error of the head relative to the reference signal. The PES is filtered with a compensation filter to generate a feed-back control signal. The feed-back control signal is combined with the feed-forward control signal to generate a VCM control signal. When the seek is done, the saved PES is processed using an iterative learning control (ILC) algorithm to adjust at least one of the reference signal and the feed-forward control signal.