The penetration of cell membrane using atomic force microscope (AFM) is studied. The penetration is monitored by AFM, and the penetration force is measured for three types of cells. The dissipated energy of the cell membrane before and after drug treatment is also calculated and analysed. Experimental results indicate that AFM is an efficient tool for measuring and monitoring the penetration of the cell membrane. Results also show that the penetration force differs significantly from each type of cells, indicating that the penetration force is a potential biomarker of cell membrane to distinguish different types of cells. Moreover, the dissipated energy of cell membrane is studied to be a biomarker to indicate the condition of the cell membrane. After the cell membrane is treated with dimethyl sulfoxide, the dissipated energy of cell membrane decreases.