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 nano manipulation, 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. Nano-imprint experiments verify the effectiveness of 3D forces sensing system and efficiency improvement of nano manipulation using this system.