Controlling the motion and its associated parameters is among the most important topics in the field of manipulation and displacement of nanoparticles. Accordingly, this article considers the control of nanomanipulation process in three general areas: 1) the distance between probe and surface, 2) the substrate, and 3) the probe of atomic force microscope (AFM). This study benefits from the adaptive fuzzy sliding-mode (AFSMC) control technique. Moreover, elliptical and cubic geometries are utilized. The results for the control of probe distance from substrate show that the system attains the acceptable value of 50 nm after 0.8 s. The desired output for the derivative of distance is fulfilled after 0.07 s. The results for the control of substrate in the horizontal direction show that for different values of λ, the desired value is obtained in different manners. The comparison between the results of this study and previous researches using the sliding mode control and proportional-integral-derivative method indicates the accuracy of the proposed method. The simulation results of the control of atomic force microscope probe for elliptical and cubic geometries demonstrate that the deviation of probe for these two geometries reaches its desired value in less than 0.04 s. However, the main difference is observed when investigating the position of atomic force microscope probe; the elliptical nanoparticle with an average radius of 75 nm has a delay of around 0.02 s for reaching the desired value compared with the cubic nanoparticle with a side length of 75 nm. In addition, the overshoot of elliptical geometry is more than that of cubic case. Finally, motion tracking along a specific path is simulated. In addition, trajectory assessment is realized on an actual experimental surface.