Semiconductor manufacturing industry has elevated cost in productions. Improvement of production efficiency is always an important goal for manufacturers. Run-to-run control has been widely used in batch manufacturing processes to reduce variations. Threaded exponentially weighted moving average (threaded-EWMA) run-to-run control is an important and stable control scheme. in this paper, we study the drifted process with mixed products are manufactured in cycles on the same tool, and find that the process outputs will be off target greatly at the beginning runs of cycle 1, 2.... if the product has a long break length. In order to reduce a possible high rework rate, a threaded double EWMA (thread-dEWMA) controller is used to handle the disturbance as well as the drift. By analysis of the system output, a drift-compensatory approach is proposed to eliminate these large deviations. In order to enhance the system performance, the well known "trade-off" solution is adopted to choose the optimal discount factors. Furthermore, how to deal with process fault is also considered in this paper. Two kinds of fault - the step fault and the ramp fault are discussed for fault tolerant approach which can reduce the large deviations of process output from the specification. Simulation study showed that the proposed approaches are effective. (C) 2009 Elsevier Ltd. All rights reserved.