The development of atomic force microscopy (AFM) opens an entirely new way to investigate the dynamic changes of cellular structures, such as cell junctions and protein molecules. Since these structures are in nanometer scale, it cannot be observed and studied by conventional optical microscopy. Besides, AFM can also be used for precise manipulation of these nano-sized molecules such that the interaction and structure-function can be studied at the single molecular level. Because of cell surface inhomogeneities and movements in living conditions, it presents a major challenge to perform the in-situ imaging and manipulation of these nanoscale biostructures. Here, we present the design and development of a biocompatible porous polymer micro-mesh for immobilizing live cells and protein molecules. Based on the novel AFM nanomanipulation and imaging system with the use of the cell fixture, the cell junctions and individual protein molecules in physiological conditions with unparalleled resolution can be easily observed and studied.