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Atomic force microscopy (AFM) is capable of producing accurate 3-D images at nanometer resolution. As a result, AFM is widely used in applications related to cell biology, such as the diagnosis and observation of tumor cells. This paper proposes phase-detection mode atomic force microscopy (PM-AFM) for the 3-D reconstruction of cell contours. The proposed three-axis scanning system employs two piezoelectric stages with one and two degrees of freedom, respectively. Accurately rendering the contours of delicate cells required a multi-input multi-output (MIMO) adaptive double integral sliding mode controller (ADISMC) in the xy-plane to overcome uncertainties within the system as well as cross-coupling, hysteresis effect, and external disturbance. An adaptive complementary sliding-mode controller (ACSMC) was installed along the z axis to improve scanning accuracy and overcome the inconvenience of conventional controllers. Phase feedback signals were also used to increase the sensitivity of scanning, while providing faster response times and superior image quality. A comprehensive series of experiments was performed to validate the performance of the proposed system.