For a few decades, molecular dynamics simulations have been employed for investigation of primary damage formation in collision cascades in solids exposed to fast particle irradiation in the nuclear stopping power regime. In most studies, radiation damage in defect-free elemental metals, alloys, intermetallic compounds, semiconductors and ceramics is considered. However, the microstructure of real materials contains grain boundaries, twins, stacking faults, dislocations and other structural inhomogeneities that affect their service properties including radiation resistance. Radiation tolerance of existing and/or newly developed materials can be adjusted by directional modification of their defect subsystem. On the other hand, nanostructuring and surface engineering by ion beam irradiation have been applied for raising service properties of a wide range of structural, functional and biocompatible materials. Therefore it is essential to gain a deeper insight into an interplay between collision cascades and structural defects including materials’ surfaces.