For AFM based robotic nanomanipulation system without displacement sensor, one of the key technical problems is to realize high accurate positioning of the AFM probe. To solve the problem, based on the hysteresis and nonlinear characteristics analysis of AFM PZT actuator, a new actuating method called "actuating method based on reappearing the scanning trajectory" is presented to actuate the PZT actuator. Then two kinds of probe positioning errors, namely kinematics coupling errors due to the tube actuator's bend motion and probe tip's positioning errors caused by cantilever deflections, are compensated to further improve the probe's positioning accuracy. Nanopatterning experiments are performed to verify the effectiveness of the new actuating method and the compensation methods of probe positioning errors