A method and system of location specific processing on a substrate is described. The method comprises establishing a gas cluster ion beam (GCIB) according to a set of beam properties and measuring metrology data for a substrate. Thereafter, the method comprises determining at least one spatial gradient of the metrology data at one or more locations on the substrate and adjusting at least one beam property in the set of beam properties for the GCIB according to the determined at least one spatial gradient. Using the metrology data and the adjusted set of beam properties, correction data for the substrate is computed. Following the computing, the adjusted GCIB is applied to the substrate according to the correction data.