Lacking real-time visual feedback is one of the main problems in working with AFM in a nano-environment. To overcome this problem, we begin to design a virtual reality environment. First, nano-image is enhanced by using image processing technique and genetic algorithms then the location and number of nano-particles and other properties are determined. A nano-manipulation environment is implemented and the forces between the tip of the probe and nano-particle are analyzed, so that we increase the ability of user in driving nano-particle in this environment. In the first step, nano-image quality will be improved by applying different filters that each one is appropriate to eliminate one type of noise. Genetic algorithms are applied to determine a suitable set of appropriate filters among filters bank, then the location and number of nano-particles will be extracted by using image processing technique. For nano-manipulation operation, the dimensions of the base plate and exact place of nano-particles on it should be defined, and the user can choose the primary and final location of the nano-particle. The second stage of simulation is driving the nano-particle in such a way that the tip of atomic force microscopy probe aims at nano-particle with constant velocity. At this moment, the movement of the tip of the probe begins, and the nano-particle moves to a chosen place, so that the user can see the manipulation process.