The factors contributing to the formation of craters on the surface of the AA6111 aluminum alloy after processing with a high-current pulsed electron beam were investigated. Microstructural studies of the crater formation area were conducted both on the surface of the irradiated layer and on the cross-sectional side. Inhomogeneity in the distribution of alloying elements was observed both across the irradiated surface and along the cross-sectional surface of the irradiated alloy layer. The regularities of crystallization of phases in the presence of various alloying elements and their effects on the formation of crater geometry were identified. The size and shape of craters were analyzed, and it was determined that the depth of all craters was less than the thickness of the layer remelted by the high-current pulsed electron beam. A mechanism was proposed whereby the formation of craters in the AA6111 alloy is the result of uneven crystallization of the surface layer melted by the high-current pulsed electron beam.