In order to accurately calculate the critical force and time of manipulation, the influence of different input parameters on output parameters should be analyzed. The EFAST statistically-based method is one of the accurate and fast methods of sensitivity analysis. Previous studies have been conducted regarding the effect of different parameters on critical force and time of two-dimensional manipulation, using various methods including graphical, differential and statistical methods. In this study, for the first time, with the use of EFAST sensitivity analysis method, the effect of six dimensional input parameters including length of cantilever, width of cantilever, thickness of cantilever, tip height, radius of nanoparticle and tip radius on eight output parameters including critical force and time of manipulation in four modes of sliding along X axis, sliding along Y axis, rolling along X axis and rolling along Y axis, is analyzed in three-dimensional manipulation. The final obtained results demonstrate that the parameter of “thickness of cantilever” is the most influential parameter on critical forces of manipulation, and the parameter of “tip height” is the most influential one on critical times.