1. A method of operating a thermal processing system comprising: positioning a wafer for processing by the thermal processing system on a hotplate comprising a plurality of zones; creating a dynamic thermal model of the thermal processing system; establishing a plurality of intelligent setpoints using the dynamic thermal model of the thermal processing system, wherein each of the plurality of intelligent setpoints is associated with a corresponding one of the plurality of zones; and reducing critical dimension (CD) variation across the wafer, profile variation across the wafer, or uniformity variation across the wafer, or a combination of two or more thereof by controlling an actual temperature of each of the plurality of zones of the hotplate using a corresponding one of the plurality of intelligent setpoints during processing.