A wafer processing system includes at least one metrology chamber, a process chamber, and a controller. The at least one metrology chamber is configured to measure a thickness of a first layer on a back side of a wafer. The process chamber is configured to perform a treatment on a front side of the wafer. The front side is opposite the back side. The process chamber includes therein a multi-zone chuck. The multi-zone chuck is configured to support the back side of the wafer. The multi-zone chuck has a plurality of zones with controllable clamping forces for securing the wafer to the multi-zone chuck. The controller is coupled to the metrology chamber and the multi-zone chuck. The controller is configured to control the clamping forces in the corresponding zones in accordance with measured values of the thickness of the first layer in the corresponding zones.