One of the major advantages of multiple-pulses Laser Thermal Annealing (LTA) with moderate energy fluence is that good dopant activation can be achieved without further increases in junction depth by successive pulses. It is demonstrated that when the laser fluence is adjusted to a value that can melt the preamorphization implantation (PAI) layer but not the underlying silicon substrate, PAI layer depths control the junction depths. Hence, it is desirable to operate LTA in this regime since this allows for a tighter process control as opposed to when the junction depth is controlled solely by the laser fluence. High Resolution Transmission Electron Microscopy (HR-TEM) micrographs show that the degree of damage repair depends on the amorphous layer thickness as well as the number of pulses. Our study allows for the evaluation of the maximum allowable PAI depth for a given number of pulses in order to fully remove the damage caused by the PAI.