As our knowledge about Nano grows we can apply Nano Technology in all fields of Science and Engineering. Molecular simulation can be used to simulate the manufacturing process in nano scale. In this paper, simulations in nano scale were investigated in two main reasons: 1- Morphology in Nano-Micro, 2-Simulation based on molecular dynamics. The basic and main aspects of both methods were explored and also a Matlab algorithm will be suggested to modeling the structure and dynamic in nano scale. First, some pieces in cylindrical and cubic forms were simulated and the effects of thermal treatment in different temperatures were investigated in light of this simulation. Second, a model based on molecular dynamics in 2D was developed to find out the effects of force exerted to AFM..