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Micro-electro-mechanical-system (MEMS)-based scanning-probe data-storage devices are emerging as potential ultra-high-density, low-access-time, and low-power alternative to conventional data storage. Nanoscale accuracy and short latency in the navigation of the probes are the primary control challenges in probe-storage applications. This paper focuses on the control design to address these challenges in a probe-based storage prototype using a micro-scanner as the nanopositioner for the storage medium. Experimental results demonstrate remarkably short seek times on the order of 1 ms for the worst-case seek operations. Moreover, a thermal-sensor-based approach is compared with a two-sensor-control configuration employing both the global-position information from the thermal sensors and the medium-derived position information. Drift and low-frequency noise can affect the performance of the thermal-sensor-based control scheme over long periods of operation. This is addressed by the second scheme, a novel control architecture based on the Hinfin control framework that uses the best measurement in each of the frequency regions.