This paper presents a new and reliable approach for in-situ imaging and manipulation of membrane protein molecules. The major problematic issue in medicine is the lack of fundamental understanding of the molecular mechanisms that cause major life-threatening and incurable diseases. The development of atomic force microscopy (AFM) opens an entirely new way to address these medical questions. A biocompatible porous polymer micro-mesh is designed for immobilizing living cells and protein molecules during AFM scanning. We demonstrate its usefulness by imaging cancerous B-cells as well as cell-junction molecules associated with living epithelial cells at high resolution. This technology can not only be used for imaging, but also for nanomanipulation. Current results suggest that this AFM nanomanipulation system and the novel cell fixture apparatus can be used to study the dynamic changes and function of cellular structures with unparalleled resolution both under physiological and pathophysiological conditions.