Molecular/atomic-level computer modeling of laser–materials interactions is playing an increasingly important role in the investigation of complex and highly nonequilibrium processes involved in short-pulse laser processing and surface modification. This chapter provides an overview of recent progress in the development of computational methods for simulation of laser interactions with organic materials and metals. The capabilities, advantages, and limitations of the molecular dynamics simulation technique are discussed and illustrated by representative examples. The results obtained in the investigations of the laser-induced generation and accumulation of crystal defects, mechanisms of laser melting, photomechanical effects, and spallation, as well as phase explosion and massive material removal from the target (ablation) are outlined and related to the irradiation conditions and properties of the target material. The implications of the computational predictions for practical applications, as well as for the theoretical description of the laser-induced processes are discussed.