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Surface cleaning of patterned wafers by batch processing has become a challenge as semiconductor fabrication moves deeper into submicron technology nodes and utilizes larger wafer sizes. Many fabrication plants (fabs) have already employed single wafer cleaning tools. A key challenge in the application of single-wafer processing tools, compared to conventional multi-wafer batch tools, is their lower throughput. Typical surface cleaning consists of exposure to a chemistry intended to remove contaminants, followed by rinsing with ultrapure water, followed by drying. To help reduce cycle time and to minimize resource consumption during rinse processes while producing a highly clean surface, a novel in situ metrology has been developed for the detection of trace residual impurities in fine structures of patterned wafers during surface preparation processes. This technology includes both hardware for in situ measurement of impurities and software for process data analysis. The technology can be used for on-line control in existing processes as well as for development and testing of new recipes and processes. In this paper, the effects of the key rinse process parameters such as water flow rate, wafer spin rate, and water temperatures are studied. Successful incorporation of this metrology into surface preparation steps will eliminate dependence on costlier and more time-consuming external analysis techniques.