Radiant energy sources enable rapid and controllable thermal processing of wafers with closed-loop control of wafer temperature. However the use of energy sources that are not in thermal equilibrium with the wafers makes the heating process sensitive to the optical properties of the wafers. In particular, patterns on wafer surfaces can cause temperature non-uniformity at length scales where lateral thermal conduction cannot smooth out the effect. Such “pattern effects” are even more significant for advanced processing techniques like millisecond annealing and pulsed laser annealing, because of the extremely large heating powers employed. The issue of pattern effects was recognized early on in the development of radiant heating technology, but has recently become a critical issue for process control. Despite the challenges, many counter-measures can be deployed to minimize pattern effects, including modifications to the wafer design, changes in processing recipe and equipment configuration. Such solutions have enabled the use of radiant heating for even the most demanding device fabrication applications.