This work lies on the framework of an interactive virtual environment for nanomanipulation. The model for the simulation of a manipulated nanoparticle dynamics in the virtual environment is constructed from the computed molecular dynamics. According to the operation by single-tip scanning probe microscope(SPM) for the nanomanipulation, the molecular forces are calculated based on the Lennard-Jones force-field such that the motion of the manipulated nanoparticles can be rendered for real-time virtual reality applications. Moreover, by coupling the CAD softwares to virtual reality (VR) techniques, the interactive virtual environment is developed for intuitive nanomanipulation visualization. Using the simulated nanomanipulation environment in VR, the operator can characterize and control the behavior of nanoparticles under the assumed SPM through physical simulation and 3D visualization.