When nano-manipulation is performed on soft samples, such as cells and biological macromolecules, an atomic force microscope (AFM) faces the drawback of lacking of real-time visual feedback. To address this issue, a visualization system for AFM-based nano-manipulation on soft samples is constructed. Specifically, the mapping relationship between the AFM topography image coordinate system and the virtual scene coordinate system is established firstly to obtain the vertex information of the sample in the virtual scene, so as to construct the virtual topography via the render of a 3-dimensional graphics engine. On this basis, a sample deformation estimation and simulation algorithm is developed based on the theory of contact mechanics, and virtual visual feedback is provided for the sample deformation caused by the probe pressing, so that the depicted virtual topography can be kept consistent with the real topography of the sample, and the topography changes on the sample surface during the pressing process can be accurately restored. The simulation and experimental results demonstrate that the designed nano-manipulation visual system can present the AFM-based nano-manipulation process in real time in the virtual scene.