Based on the review of previous experimental and theoretical studies on the surface processing by a pulsed intense electron beam, the induced temperature field in aluminum and 304 stainless steel is simulated by the finite element method (FEM) to estimate the existing time and depth of molten metal flow field on the irradiated surface. The generation of craters is attributed to the thermal resistance formed by the grain boundaries, and the influence of material properties on the mechanism of crater evolution is also discussed. Two-phase flow field simulation on molten metal is carried out with a combination of level-set method and FEM to estimate the mass transfer behavior at the craters and surface protuberance. It is revealed that the mass transfer effect driven by surface tension is an important factor for the formation and evolution of round-shaped craters on the surface of metals with high melting point, viscosity and surface tension coefficient. However, for metals with low melting point, due to the strong disturbance by ablating gas plume and low surface tension effect, the craters are more likely to have irregular splashing edges.