The research on semiconductor materials has attracted significant interest of researchers in the last few decades, due to their applications in numerous industrial sectors as well as in common life. Particularly, the investigation of these compounds has been improved with the support of the computational model theory. This chapter discusses the application of Molecular Dynamics, a classical computational approach, in the analysis of significant three-dimensional (3D) semiconductor material systems, emphasizing III-V and CIS (copper, indium or gallium as well as sulfur or selenium) families. Specifically, the growth processes and their thermodynamics phenomena are focused on the Molecular Beam Epitaxy (MBE) technique. In addition, this chapter provides considerations about the structural properties. We examine the evolution of the growth process and several important characteristics of the model that provides fundamental information on the structural defects.