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This paper addresses the design and application of an observer-based nonlinear controller employing a CMOS-MEMS nano-Newton force sensor. The sensor is designed using AMI 0.5μm 3-Metal 2-Polysilicon CMOS technology capable of sensing an out-of-plane force perpendicular to the probe tip; it is suitable for biomedical applications that measures external force excitation of less than 100 Hz. Measurement errors occur when there are in-plane movements of the probe tip; these errors can be controlled by the actuators incorporated within the sensor. Observer-based controller is necessitated in real-world control applications where not all the state variables are accessible for on-line, real-time measurements, and/or where the measurements are corrupted by noise.