The sensitivity analysis of atomic force microscope (AFM) based manipulation of gold spherical nanoparticles in air medium has been carried out in previous research works. In the AFM-based manipulations conducted in various biological liquid mediums, the new environmental parameters associated with these biological fluids also affect the dynamics of the manipulation process. Therefore in this research, the Sobol sensitivity analysis method has been employed to find out how these new parameters as well as the other effective parameters influence the manipulation process. The parameters have been classified into two groups of AFM parameters and environmental parameters. According to the obtained simulation results, in the group of AFM parameters, cantilever thickness (with a sensitivity index of 57%) is the most sensitive parameter in the manipulation of cylindrical biological micro/nanoparticles, followed by the parameters of cantilever length and cantilever width. By examining the sensitivity of environmental parameters for cylindrical biological micro/nanoparticles in biological mediums, it is observed that the highest sensitivity belongs to the dimensional parameters of target particles (the most sensitive environmental parameter is cross-sectional radius of target particle with a sensitivity index of 52%), followed by the sensitivity of adhesion work in the biological medium of manipulation. It is found that the critical force for the onset of movement increases substantially with the increase in the cross-sectional radius of target particle, ratio of particle length to its cross-sectional radius and also with the increase in the work of adhesion in the biological environment.