This work aims to systematically gain an understanding of the effects of multilayer patterns on wafer temperature uniformity during rapid thermal processing (RTP) and to explore possible solutions to the problem. The radiative properties of patterned wafers are predicted using electromagnetic multilayer theory, including a model for the temperature-dependent optical constants of silicon for wavelengths greater than 0.4 mu m. The model for predicting radiative proper-ties is coupled to a finite element-based reactor transport model to predict steady-state and transient wafer temperature distributions. A generic two-dimensional axisymmetric single-side illumination RTP system is used as a test bed to explore pattern effects. Realistic examples of shallow junction annealing and titanium silicidation are simulated. Results show that pattern effects are an important consideration for rapid thermal processes and that wafer processing, front and back side illumination, and reactor design all have significant effects on pattern-induced temperature nonuniformity.