This paper focuses on the modification of the PLS (partial least squares) modeling. The new method allows incorporation of a dEWMA (double exponentially weighted moving average) control algorithm into the standard run-to-run controller design for semiconductor processes. The resulting structure of the PLS model can extract the strongest relationship between the input and the output variables. It is particularly useful for inherent noise suppression. In addition, the resulting non-square MIMO control system can be decomposed into a multi-loop control system by employing pre-compensators and post-compensators of the PLS model, which is constructed from the input and output loading matrices. Subsequently, the conventional dEWMA controller can be separately and directly applied to each SISO control loop. The performance of the proposed method is illustrated through a chemical-mechanical polishing process in the manufacturing of the semiconductor. (c) 2006 Elsevier Ltd. All rights reserved.