It still remains as a challenge to design functions of self-assembled materials in a predictable manner because of the lack of understanding on self-assembly processes at a molecular level. Here we demonstrate new electron microscopic techniques for high-resolution imaging of organic materials based on the chemical design of supporting substrates for specimen molecules. The new analytical approach allowed us to study the time evolution of the structures of individual molecules in the self-assembled structures without significant decomposition under irradiation of an electron beam. Based on the knowledge obtained by the microscopic imaging, we achieved structure control of a variety of functional self-assembled structures ranging from organic particles to bilayer membranes, which were utilized for device and medicinal applications.