We review atomistic modeling approaches for issues related to ion implantation and annealing in advanced device processing. We describe how models have been upgraded to capture physical mechanisms in more detail as a response to the accuracy demanded in modern process and device modeling. Implantation and damage models based on the binary collision approximation have been improved to describe the direct formation of amorphous pockets for heavy or molecular ions. The use of amorphizing implants followed by solid phase epitaxial regrowth has motivated the development of detailed models that account for amorphization and recrystallization, considering the influence of crystal orientation and stress conditions. We apply simulations to describe the role of implant parameters to minimize residual damage, and we address doping issues that arise in non-planar structures such as FinFETs.