In this paper we discuss some of the issues involved in the modeling of damage evolution, dopant diffusion and electrical activation as a result of ion implantation and annealing processes in Si. Dopant diffusion and activation during thermal anneal is complicated by the presence of the damage generated by the energetic impinging ion. Of particular interest is the case of B, as it is the most common dopant used for the formation of p+ junctions. We review the correlation between defect evolution and B diffusion and B clusters, both for sub-amorphizing and amorphizing implants. The effects of implant parameters and annealing conditions will be analyzed. Although we concentrate on Monte Carlo modeling, links to more detailed ab initio and molecular dynamics simulations as well as continuum modeling and experiments complement this analysis.