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Recent dramatic progress in studying various two-dimensional (2D) atomic crystals and their heterostructures calls for better and more detailed understanding of their crystallography, reconstruction, stacking order, etc. For this, direct imaging and identification of each and every atom is essential. Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) are ideal and perhaps the only tools for such studies. However, the electron beam can in some cases induce dramatic structure changes, and radiation damage becomes an obstacle in obtaining the desired information in imaging and chemical analysis in the (S)TEM. This is the case of 2D materials such as molybdenum disulfide MoS2, but also of many biological specimens, molecules, and proteins. Thus, minimizing damage to the specimen is essential for optimum microscopic analysis. In this article we demonstrate, on the example of MoS2, that encapsulation of such crystals between two layers of graphene allows for a dramatic improvement in stability of the studied 2D crystal and permits careful control over the defect nature and formation in it. We present STEM data collected from single-layer MoS2samples prepared for observation in the microscope through three distinct procedures. The fabricated single-layer MoS2samples were either left bare (pristine), placed atop a single-layer of graphene, or finally encapsulated between single graphene layers. Their behavior under the electron beam is carefully compared, and we show that the MoS2sample “sandwiched” between the graphene layers has the highest durability and lowest defect formation rate compared to the other two samples, for very similar experimental conditions.