Methods for controlling substrate uniformity in a thermal processing chamber include a measuring process to provide temperature-related quantities across a radius of a substrate, correlating substrate properties with processing parameters to simulate deformation of the substrate at various radial distances over a temperature range, a thermal process so that temperature of at least one reference region within the substrate matches a target set point temperature, measuring a temperature of at least one reference region as the substrate rotates, measuring deformation of the substrate as the substrate rotates, correlating measured temperatures of at least one reference region with simulated deformation of the substrate and measured temperature-related quantities of the substrate to calculate a simulated shape change of the substrate over a temperature range, tuning substrate flatness by adjusting lamp temperature profile across the substrate based on simulated shape change of the substrate and actual shape of the substrate.