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Atomic force microscope (AFM) has been proven to be a useful tool to characterize and change the sample surface down to the nanometer scale. However, in the AFM based nanomanipulation, the main problem is the lack of real-time sensory feedback for a user, which makes the manipulation almost in the dark and inefficient. In this paper, the AFM probe micro cantilever-tip is used not only as an end effector but also as a three dimensional (3D) nano forces sensor for measuring the interactive forces between the AFM probe tip and the object or substrate in nanomanipulation. The nano forces acting on cantilever-tip is modeled and the real-time PSD signals are used to calculate the forces. With new parameters calibration method used, the real 3D nano forces can be easily got and then fed to a haptic/force device for operator to feel, thus real-time manipulation forces information is obtained, with which the efficiency of nanomanipulation can be significantly improved. Nanoimprint experiments verify the effectiveness of 3D forces sensing system and efficiency improvement of nanomanipulation using this system.