We focus this work on multi-scale modeling of the ion-beam-induced amorphization and recrystallization in Si, although our scheme can be applied to other materials. We use molecular dynamics to study the formation mechanisms of amorphous regions. We have observed that along with energetic ballistic collisions that generate Frenkel pairs, low energy interactions can produce damage through the melting and quenching of target regions. By quantifying these results, we have developed an improved binary collision approximation model which gives a damage description similar to molecular dynamics. We have successfully applied our model to ion and cluster implantations. In order to define the energetic of defects in a more computationally efficient Kinetic Monter Carlo code, we have used molecular dynamics results related to the recrystallization behavior of local amorphous regions. The combination of all these simulation tools, molecular dynamics (fundamental studies of damage formation and recrystallization), improved binary collisions (including ballistic and melting-related damage) and Kinetic Monte Carlo (for efficient defect kinetics modeling during the implantation and the subsequent annealing), allows us to model the effect of ion mass, beam current and implant temperature on the amount and morphology of residual defects in Si.