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The exponentially weighted moving average (EWMA) controller is a very popular run-to-run (RtR) control scheme in the semiconductor industry. However, in any typical step of semiconductor process, many different products are produced on parallel tools. RtR control is usually implemented with a ldquothreadedrdquo control framework, i.e., different controllers are used for different combinations of tools and products. In this paper, the problem of EWMA controller tuning and performance evaluation in a mixed product system are investigated by simulation and time-series analysis. It was found that as the product frequency changed, the tuning guidelines of a threaded EWMA controller were different for different types of tool disturbances. For a stationary ARMA(1,1) noise, the tuning parameter lambda should be decreased as product frequency decreases. If the tool exhibits nonstationary tool dynamics, e.g., ARIMA(1,1,1) noise, the tuning parameter should increase as the product frequency decreases.