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Desmosomes are cell-cell junctions that provide mechanical strength for cells and maintain integrity of tissues in animal skins and hearts. Disruption of the desmosome like in some autoimmune diseases will therefore change the mechanical property of the anchoring cells and causing blistering. In the paper, we used Atomic Force Microscopy (AFM) to visualize the keratinocytes intercellular structure. The AFM based nanomanipulation system is employed to perform the nanoindentation experiment for measuring keratinocytes nanomechanical property under both physiological and pathophysiological conditions. Our demonstration of the use of AFM for in situ imaging and nanomanipulation for quantifying stiffness in nanoscale can facilitate the investigation of diseases related to blistering and development of therapeutic strategies accordingly.