Since its introduction, the atomic force microscope (AFM) has developed into a ubiquitous tool for 3D imaging and manipulating objects at a nanoscale level. However, the imaging performance of AFMs is limited because of the limitations of its scanning unit, i.e., piezoelectric tube scanner (PTS). This paper addresses the design and experimental implementation of a two-input two-output (TITO) model predictive control (MPC) scheme which aims to overcome the limiting factors of the PTS in order to achieve improved 3D images. The effectiveness of the proposed method is experimentally compared with the existing AFM proportional-integral (PI) controller, the resonant controller, and the single-input single-output (SISO) MPC controller.