Two dimensional (2D) layered structures, such as graphene and transition metal dichalcogenides (TMDs), have attracted much attention for future electronics and optoelectronics due to their unique electronic structures. The properties of 2D materials are strongly influenced by their atomic structures. Visualizing their structural and chemical configuration at atomic scale is thus essential to understand and further control their final properties. Recently a low-voltage aberration corrected transmission electron microscopy (LVAC-TEM) has been intensively developed and recognized as the most powerful technique giving an atomic scale imaging of one or few atom thick layer materials, which provides precise local structural information such as vacancies and dislocations. In addition, this technique also allows to modify the atomic structure in 2D layers by electron irradiation. Therefore, we are able to follow atom displacements during the defect formation to study their dynamics. In this talk, LVAC-TEM characterization techniques for the study of 2D materials concerning their defects, strain, dopants and further dynamics will be demonstrated and how these structural analysis can contribute to the domain of 2D engineering will be discussed.