The presented work presents the results of molecular dynamics modeling of changes in the surface layer of the computational cell under a short-term high-energy impact. Interest in this topic is because the processes occurring in the surface layer, which is in a liquid state, will subsequently have an impact during its crystallization, and, as a result, will affect various physical and geometric characteristics of the surface of the material as a whole. The model constructed and described in the work, in which the temperature of the computational cell is distributed in accordance with the solution of the linear problem of heat conduction, made it possible to reveal the discontinuity of the surface layer, which consists in the localization of excessfree volume in the form of a group of spherical pores. The sizes of these imperfections, as well as the duration of their existence, have differences when modeling different energy densities of laser radiation. Further research made it possible to reveal the conditions under which the pores remain stable throughout the entire simulation time, as well as to reveal the relationship between the crystallographic orientation of the “solid-liquid” interface and the sizes of the formed pores.