Rapid thermal annealing methods and systems for annealing patterned substrates with minimal pattern effect on substrate temperature non-uniformity are provided. The rapid thermal annealing system includes a front-side heating source and a backside heating source. The backside heating source of the rapid thermal annealing system supplies a dominant amount of heat to bring the substrate temperature to the peak annealing temperature. The front-side heating source contributes to heat up the environment near the front-side of the substrate to a temperature lower than about 100° C. to about 200° C. less than the peak annealing temperature. The asymmetric front-side and backside heating for rapid thermal annealing reduce or eliminate pattern effect and improve WIW and WID device performance uniformity.