Only after the invention of the atomic force microscope (AFM), measurement of single molecule mechanical properties of DNA and proteins became possible. Until then, single molecule mechanical properties were of theoretical interest but difficult to be measured. The rigidity, toughness of individual protein molecules or the strength of protein-protein interactions has become a popular subject since then. In this article, 1) the single molecule mechanics of α-helical polypeptide, 2) force spectroscopy of pulling membrane proteins from red blood cell surface, and 3) a new method of hole creation with controlled positioning and size on the live cell surface are reviewed as examples of recent development from our laboratory. By exploiting more diversified uses of the probe modification, the AFM based technology will be brought to a stage with many more routine applications in biological field.