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This report describes the realization of an embedded hardware system designed to perform fast control for an atomic force microscope (AFM). Traditional implementation of control algorithms for AFMs, either PC-based or DSP-based, does not meet the high-speed scanning requirement. Considering the capability of parallel computing, FPGA is employed to achieve real-time control for an AFM equipment. Specifically, in the designed embedded system, the hardware includes several key components of signal acquisition, signal conversion, data communication as well as the FPGA-based control law implementation. Besides higher control frequency, the designed FPGA-based embedded system provides a general platform for different advanced control strategies, on which a variety of control algorithms can be implemented and tested conveniently by replacing the codes in the software rather than changing hardware structure, due to the merit that FPGA can integrate internal CPU and it has a large number of logic cells and soft-cores. The widely utilized proportional-integral- derivative (PID) algorithm is chosen as an example to demonstrate the implementation of a controller by using powerful hardware description tools.