Atomic force microscopy (AFM) obtains a high resolution at nanometer. In the current study, we found that, before and after adding CD34, CD44 or CD29 antibodies, the AFM images of mouse adipose tissue derived mesenchymal stem cells (ADMSCs) had significant changes in both cell morphous (shape) and the average roughness of cell membrane. However, there was no significant difference in the cell shape and the average roughness of cell membrane, after adding CD45 or CD144 antibodies. Therefore, we could use the AFM to scan cell shape or to calculate the average roughness changes of cell membrane to analyze the existence of cell membrane antigen qualitatively.