Ion implantation is a very well established technique to introduce dopants in semiconductors. This technique has been traditionally used for junction formation in integrated circuit processing, and recently also in solar cells fabrication. In any case, ion implantation causes damage in the silicon lattice that has adverse effects on the performance of devices and the efficiency of solar cells. Alternatively, damage may also have beneficial applications as some studies suggest that small defects may be optically active. Therefore it is important an accurate characterization of defect structures formed upon irradiation. Furthermore, the technological evolution of electronic devices towards the nanometer scale has driven the need for the formation of ultra-shallow and low-resistive junctions. Ion implantation and thermal anneal models are required to predict dopants placement and electrical activation. In this article, we review the main models involved in process simulation, including ion implantation, evolution of point and extended defects and dopant-defect interactions. We identify different regimes at which each type of defect is more relevant and its inclusion in the models becomes crucial. We illustrate in some examples the use of atomistic modeling techniques to gain insight into the physics involved in the processes as well as the relevance of the accuracy of models.