In nanomanipulation using atomic force microscopy, for the displacement of various micro/nanoparticles, calculation of accurate critical force and time of manipulation in order to not damage and precise manipulation of micro/nanoparticles, is necessary. To achieve this goal requires accurate modeling of kinematics and dynamics of a two-dimensional nanomanipulation that already has been done. In this paper, three-dimensional nanomanipulation modeling and simulation dynamic has been done for more simulation results closer to the results of real nanomanipulation. For this purpose, by taking a spherical shape for micro/nanoparticle, three-dimensional kinematic relations manipulation extracted. Then, JKR contact model for use in manipulation provided and rectangular beam stiffness equations derived in three dimensions. In the final stage of the modeling of the dynamics of the three-dimensional micro/nanoparticles to extract force equations and critical time manipulation obtained. Then the equations obtained by simulation, three-dimensional manipulation amount of force and critical time for both DNA and platelets biological particle is calculated. The results indicate start rolling motion of the particles studied before rolling around on the x-axis and y axis and z as well as the critical need for displacement of particles of the platelet-derived DNA.