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An atomic force microscope (AFM) based system has been built for the manipulation of materials at the nanometer scale. The AFM is combined with an inverse optical microscope and an UV-laser microbeam system for photoablation. The actuators of the AFM are controlled using a digital signal processor. Real-time routines and a graphical user interface have been programmed for high resolution imaging and nanomanipulation. The nanomanipulation can be pre-programmed offline or directly performed using a low-cost haptic interface. In this paper, we discuss the whole system and the different methods for manipulation.