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You can only ask one question at a time so I edited down accordingly. SEM stands for scanning electron microscope. It is among the most advanced microscopic instruments and techniques in the world today. It can be used to visualize surface details of a sample down to the nanometer range (10^-9 meters). But individual chemical bonds are measured in the picometer range (10^-12 meters), so a scanning electron microscope cannot be used to see individual atoms in a chemical sample. The only real method to directly view various atoms directly in 3D space is X-ray crystallography. This technique uses X-rays on crystalline solid samples to view their arrangement in 3D space, thus inferring the different chemical bonds and the structure of the molecule as a whole.
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