Atomic force microscope (AFM) is equipped with height recognition with nano and sub-nano meter scale, and it can accurately build three-dimensional (3D) imaging of samples with micro-structure. In this paper, we propose a homemade phase-detection mode atomic force microscopy (PM-AFM). In measuring system, here we use a compact CD/DVD pick-up-head to measure the cantilever deflection. In scanning system, we use piezoelectric stages as the planar scanner. For the sake of accurately obtaining the contour of tender cells, first we design an MIMO adaptive double integral sliding mode controller (ADISMC) in xy-plane to increase the positioning accuracy and provide precision cell size. Second, in z-axis we design an adaptive complementary sliding-mode controller (ACSMC) to improve the scanning accuracy and to overcome the inconvenience for user with traditional proportional-integration controller. Besides, we use phase feedback signal, which features with higher sensitivity and faster response. Finally, the extensive experimental results are used to validate the performance of the proposed controller, quantify the scanning image quality of standard grating and reconstruct cells topography.