In this paper, the vibration behavior of atomic force microscopy (AFM) micro-cantilever (MC) with a piezoelectric layer in the non-contact mode considering the axial load in the air medium was studied. In the dynamic modes of AFM nano-robot, parameters such as amplitude, frequency and motion phase are used as feedback factors in the control system in order to extract sample surface information and the nanoparticle voltage. Consequently, to extract these parameters, the vibration analysis of the MCs of this nano-robot is essential. Additionally, because of the wide-spread applications of oblique MCs, applying the axial and transverse forces into the model is absolutely necessary. In order to simulate the AFM four-layered piezoelectric MC with the axial displacement, Timoshenko beam theory as well as modified couple stress theory has been used. Considering the axial displacement in the modeling not only leads to more degrees of freedom, but also has increased the amount of calculations. To extract the equations of the system, energy method has been used, and then, the FEM was applied to discrete the equations. To verify the accuracy of the results, the frequency and time responses of FEM have been compared with the results of the 3D mode simulation obtained by COMSOL software and experimental results. The comparison of results indicates that modifying the modeling by considering the axial displacement has increased the accuracy of the frequency and time responses. The error percentage of the first frequency response is 0.42% and the error percentage of the time response is 0.0053%. Furthermore, to examine the effect of MC geometry on its vibrational behavior, frequency and time responses of three common geometries of AFM MCs have been extracted. The results illustrate the improvement of modeling in all three geometries. Then, the sample surface topography of MCs at the first and second excitation frequencies in contact with rectangular roughnesses demonstrated the decline of time delay at the second excitation frequency. The results of the topography simulation in the air environment show that the roughness's trend is better at the second mode than at the first mode. Finally, the effect of MC angle on the topography of the rectangular MC surfaces in contact with the rectangular roughness in 2D and 3D modes was examined in the presence and the absence of axial load. The results show that in the presence of the axial displacement in modeling, by increasing of MC angle, the topography quality increases drastically.