An equalizer employed in conjunction with bit-patterned media (BPM) is designed to take advantage of a common topology associated with BPM in which each data track is comprised of a plurality of sub-tracks. The equalizer-target filter pair is designed as multiple-input/multiple-output (MIMO) system, in which the readback signal is divided into readback signals associated with each sub-track. The MIMO equalizer takes into account differences in the channel response associated with each sub-track. A detector is configured to receive a plurality of equalized inputs provided by the MIMO equalizer, wherein the detector generates in response estimates of the user data stored on each of the plurality of sub-tracks.