In this paper we present a computational tool for the simulation of laser annealing processes in FinFET structures. This is a complex self-consistent problem, where heating is evaluated by means of the time harmonic solution of the Maxwell equations. The main features of our computational code include: A versatile graphical user interface for the structure design; The assignment of materials and the simulation analysis; An interface with the finite element method solver for the automatic generation of the mesh and the runtime control; Parameters for numerous materials (optical/thermal properties and mass transport) as a function of temperature and phases; An efficient coupling with electromagnetic simulations for the self-consistent source estimate (i.e. the power dissipation) in nanostructured topographies; Experimental validation of nanostructured samples; Multiple-do-pant models simulating dopant redistribution, including diffusion solubility and segregation; Alloy model, e.g. SiGe (where the melting point depends on the alloy fraction); Multiple phases (e.g. amorphous, liquid, crystal). As a particular application of the tool we present a study of the laser process design by varying the laser fluence, polarization of the electromagnetic field and the pitch of the devices. Results are in excellent agreement with the experiment and could serve as guidelines for the realization of targeted laser annealing processes.