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In scaling-up Carbon Nanotubes (CNTs) array manufacturing, the uniformity of CNTs' height, or flatness of array, is critical for the yield of nanodevices fabricated from CNTs, and thus needs to be properly controlled. However, since the flatness of the CNTs array is better characterized by a profile, the conventional run-to-run (R2R) controllers that are designed for a single or multiple quality indicators are not effective in controlling the CNTs array manufacturing process. Therefore, in this work, we first develop a statistical model to characterize the variation of the flatness profile, and then derive a novel R2R profile controller based on a state-space model and Kalman filter to improve the flatness of CNTs array. The performance of the proposed R2R control algorithm is studied and compared with existing controller via simulation studies.