When live endothelial cells imaged using atomic force microscopy (AFM), distortion of the cell shape could be caused by the interaction between the probe and cell membrane, which depends on the force and the scanning speed used. In this study, a shape recovering method was developed. Two forces were considered in the method: the vertical and the lateral force of the tip exerted on the cell membrane during the scanning. The cell membrane was modeled as an elastic material. Results show that the recovering is necessary to reveal the original cell shape. The AFM tip effect should be taken into consideration in the live cell morphological study using AFM.