The reported study discusses the formation of micro- and nanocrystalline surface layers in alloys on the example of Ti-Y and Al-Si-Y systems irradiated by electron beams. The study has established a crystallization mechanism of molten layers in the micro-and nanodimensional range, which involves a variety of hydrodynamic instabilities developing on the plasma–melt interface. As suggested, micro- and nanostructures form due to the combination of thermocapillary, concentration and capillary, evaporation and capillary and thermoelectric instabilities. This mechanism has provided the foundation for a mathematical model to describe the development of structures in focus in the electron beam irradiation. The study has pointed out that thermoelectric field strength E ≥ 106 V/m is attributed to the occurring combination of instabilities in micro- and nanodimensional ranges. A full dispersion equation of perturbations on the melt surface was analyzed.