In this paper, we present a discrete-time modified sliding mode proximate time-optimal servomechanism (MSMPTOS) applied to scanning probe microscope (SPM)-based data storage (SDS) systems. Three conditions on the global asymptotic stability are introduced. Time-varying sliding mode with variable convergence rate factor is used to eliminate the overshoot problem and reduce the settling time compared to the conventional sliding mode proximate time-optimal servomechanism (SMPTOS). For long track seek, its trajectory is bounded by a velocity profile that is close to time-optimal velocity profile. Its settling performance is hardly affected by seek distance whereas reducing seek time. We have obtained improved seek performance over SMPTOS for short and long seeks. Its effectiveness is verified with simulation results.