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 an operator, which makes the manipulation almost in the dark and inefficient. For solving this problem, the AFM probe micro cantilever-tip is used not only as an end effector but also as a 3D nano forces sensor for sensing the interactive forces between the AFM probe tip and the object or substrate in nanomanipulation, and a kind of new and relatively easier parameters obtainment or calibration method in forces calculation has also been presented. In addition, for further improving probe positioning accuracy with a sample-scanning AFM, two important errors in probe positioning are quantitatively analyzed according to the tube scanner kinematics model presented in this paper, corresponding methods are adopted for minimizing the two errors and thus the probe positioning accuracy can be greatly improved. With 3D nano forces sensing through a haptic/force device and probe positioning accuracy improvement, the efficiency and accuracy of nano manipulation can be significantly improved. Experiments are presented to verify the effectiveness of the nanomanipulation system.