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In order to improve productivity in the photolithography process of high-product mix/low-volume factories, an automated stepper load balance allocation system was developed. The system enables us to maintain a balanced load distribution of tool constraint layers among all steppers. We developed a processing time estimation function and a load balance allocation function. The processing time estimation function calculates accurate loads based on the processing times related to the product, the process layer, and the stepper. The load balance allocation function was realized by applying a dynamic programming method. The system has decreased the deviation in the total processing time among all steppers by 10%, compared to the conventional manual allocation method.