Important recent advances in transmission electron microscopy instrumentation and capabilities have made it indispensable for atomic-scale materials characterization. At the same time, the availability of two-dimensional materials has provided ideal samples where each atom or vacancy can be resolved. Recent studies have also revealed new possibilities for a different application of focused electron irradiation: the controlled manipulation of structures and even individual atoms. Evaluating the full range of future possibilities for this method requires a precise physical understanding of the interactions of electrons with energies as low as 15 keV now used in (scanning) transmission electron microscopy, becoming feasible due to advances both in experimental techniques and in theoretical models. We summarize the state of current knowledge of the underlying physical processes based on the latest results on two-dimensional materials, with a focus on the physical principles of the electron-matter interaction, rather than the material-specific irradiation-induced defects it causes.
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