Efficiency and accuracy of AFM-based nanomanipulation are still major problems to be solved,due to the nonlinearities and uncertainties,such as drift,creep,hysteresis,etc. The deformation of cantilevers caused by manipulation force is also one of the most major factors of nonlinearities and uncertainties. It causes difficulties in precise control of the tip position and causes the tip to miss the position of the object. In order to solve this problem,the traditional approach is to use a rigid cantilever. However,this will significantly reduce the sensitivity of force sensing during manipulation,which is essential for achieving an efficient and reliable nanomanipulation. In this paper,a kind of active AFM probe has been used to solve this problem by directly controlling the cantilever’s flexibility or rigidity during manipu-lation. Based on Euller-Bernoulli Model,a kind of controller of the active probe employing Peri-odic-Output-Feedback(POF)law is implemented. The results of simulation and experiments have demonstrated that this theoretical model and POF controller are suitable for precise position control of nanomanipulation.