The simulation of laser annealing, applied to the formation of ultra-shallow junctions in Si, is discussed. Our effort is developing tools capable to aid the process integration issue. The numerical approach deals with a double problem: 1) the interaction between the irradiated transistor structure and the laser light, 2) the non-equilibrium evolution of the thermal field, molten regions and dopant density. Here we present a complete methodology: the calculated heat source distribution, induced by the irradiation, is used as input of a phase-field approach for the simulation of the thermal phase and impurity fields. We solved numerically the phase field equations in two dimensional structures, considering as an initial status the generic material modification due to an ion implant process. We present various simulation results obtained in MOS structures with different geometry. With the support of the simulation results we discuss the problematic and the perspectives of the excimer laser annealing process application in the fabrication of MOS devices.