Electron microscopy has greatly contributed as a powerful tool in both the characterization and identification of materials in the atomic scale. In these contributions, the most important advantage is it's ability for dynamic study of phenomena, i.e.,in situexperiments. This research has been carried out using high voltage electron microscopes, but some results have been obtained with high resolution electron microscopes under critical conditions. Electron microscopy has been improved further to become an indispensable “Micro-Laboratory” in which formation of various advance materials can also be carried out precisely in the atomic scale. Electron beam science and engineering is a typical example in this research field, and detailed processes of crystalline-amorphous transition and electron irradiation induced foreign atom implantation have been clarified by this method. Recently, new applications to the research fields of non-linear material behavior, such as the behavior of atom clusters and the role of electric dipoles on diffusion, have been carried out.