Abstract-Advanced process control (APC) has been recognized as a proper tool for maximizing profitability of semiconductor manufacturing facilities by improving efficiency and product quality. Run-to-run (RtR) process control with good quality and reliable performance for APC applications are most applicable. This paper proposes a new RtR control scheme, tool based disturbance estimator (TBDE) control scheme, which is adaptive to the mixed product overlay processes. The TBDE control scheme which employs threaded double exponential weighted moving average (d-EWMA) with the drift compensation scheme to deal with the disturbance caused by tool-induced drift and product-induced shift. The method is applied to the estimation of overlay parameters in mixed product lithography overlay process. The experimental results revealed that application of the TBDE is proven to significantly improvement in the mixed product overlay process.Index Terms-Advanced process control, run-to-run, overlay, mixed product, TBDE control scheme.