The electronics boom happened with the invention of semiconductor materials with Si becoming the number one in the race. But now, since Si electronics seems to be reaching its limit, the researchers are switching their attention to 2D materials because of their unique electrical, mechanical, or optical properties. Transition metal dichalcogenides (TMDs) are semiconductor materials from this family that show promise to be the next generation of nanoelectronics as well as give possibility to improve energy or informational storage. However, for maintaining high efficiency, the structure of TMDs should have minimum number of defects, misfits, or inclusions of other elements. This indicates a need to understand the structural and elemental composition of the 2D materials to atomic scales, and this is where techniques like (scanning) transmission electron microscopy (S)TEM and energy-dispersive x-ray spectroscopy (EDX) come to aid. In this study, we will discuss sample preparation and analysis techniques for of SnSe, MoS2, WS2, WSe2, and graphene/Al heterostructures on silicon wafer and sapphire substrates, the methods of uncovering the elemental and layer composition of these materials and provide image and signal processing approaches to increase the signal-to-noise ratio of the currently employed techniques. All of these will help us reach a conclusion about atomic structure and elemental composition of the materials and show the possible traps and pitfalls that a microscopist might encounter during similar analysis for either TMDs or other types of 2D materials.