A method of compensating for across-wafer variations in photoresist thickness is provided. The method comprises providing a wafer having a process layer formed there-above, forming a layer of photoresist above the process layer, measuring a thickness of the layer of photoresist at a plurality of locations to result in a plurality of thickness measurements, providing the thickness measurements to a controller that determines, based upon the thickness measurements, an exposure dose of an exposure process to be performed on the layer of photoresist, and performing the exposure process on the layer of photoresist using the determined exposure dose. This exposure dose may be varied on a flash-by-flash basis as the stepper tool “steps” across the surface of wafers. That is, the exposure dose for a group of flashes, or for each flash, may be varied in response to the thickness measurements.