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Whenever we try to enhance the production yield, we have problems identifying the cause of invisible defects over the entire process, even more so for charge-coupled devices (CCD). This time, we utilized the Mahalanobis Taguchi System (MTS) method with several original techniques to identify the cause of failure in the wafer process. We calculated the historical data of CCDs process parameter and took several countermeasures. According to the results, we learned that the invisible defects corresponded to the contamination of organic matter and the front-end process's sensitivity.