Process Window Qualification (PWQ) is a well-known wafer inspection technique used to qualify the IC manufacturing lithography process window. Circuit designs are becoming denser and more complex in advanced semiconductor process technologies. Therefore, yield is becoming increasingly sensitive to defects. How to detect wafer defects at an early stage is the key to improving wafer yield. Additionally, shortening the PWQ total turn around run time is an important factor for a wafer yield improvement methodology. In this paper, the Winbond OPC team and Cadence Pegasus DFM team initiated a project to improve the PWQ run time and accuracy using a pattern analysis flow. This flow includes defect data pre-processing, classification, and filtering, including the use of CD-SEM image auto-alignment to improve extraction locations and wafer results. The huge data volumes are reduced in order to create easy to review results. This flow reduces the PWQ processing time and correctly finds real wafer defects to improve process windows and yield.