Previous studies of the effects of the interaction of electron beams with bilayers of amorphous chalcogenides and metals such as silver and copper have shown that the type of pattern formed by electron beams scanned across these bilayers is dependent on the energy of the electron beam and on the thickness of the bilayer. Whether these bilayers are freestanding or are deposited on a substrate has also been shown to be important. The purpose of this investigation is to develop a model to explain how the electron-beam energy and bilayer thickness as well as the physical processes produced by the electron beam can lead to different types of pattern. These processes include radiolysis, secondary electron generation and the formation of superionic silver chalcogenide phases. With high electron-beam energies and thin freestanding bilayers, these processes are central to the formation of the metal-free patterns generated in thin freestanding bilayers in a scanning transmission electron microscope. Silver patterning on the surface of thick bilayer films in a scanning electron microscope using less energetic electron beams has also been shown to depend on a mechanism involving the neutralising of silver ions produced by radiolysis with secondary electron generation. This model has also been used to explain the dependence of the type of pattern formed on the incident electron energy when silver/amorphous chalcogenide bilayers of a thickness suitable for X-ray mask production are exposed to an electron beam with energies over the 5–30 keV range.