Nowadays, with the growing use of AFM (Atomic Force Microscope) nanorobots in the fabrication of nanostructures, research in this area has been proliferated. The major limiting of manipulation process is the lack of real-time observation. Computer simulations have been widely applied to improve the feasibility of the process. The existing 2D strategies are incapable of presenting the feasibility of the process. Therefore, 3D simulations of effective forces during the manipulation process and the control mechanism of the process have been presented in this research, where the effective parameters are investigated. To evaluate the validity of the presented results, a FEM simulation is proposed. It is observed that the two sets of results (the analytical method and the finite element approach) have adequate correlation, while the discrepancy which is in an acceptable range, is due to the different solving technique of the finite element method. By applying the presented models, it is now possible to accurately predict the effective forces for fabricating the nanostructures.