In the recent years threaded run-to-run (RtR) control algorithms have experienced drawbacks under certain circumstances, one such trait is when applied to high-mix of products such as in Application Specific Integrated Circuits (ASIC) foundries. The variations in the process are a function of the product being manufactured as well as the tool being used. The presence of semiconductor layers increases the number of times the lithography process must be repeated. Successive layers having different patterns must be exposed using different reticles/masks in order to maximize tool utilizations. The objectives of this research are to develop a set of methodologies for evaluation and extension of threaded control applied to overlay. This project defines methods to quantify the efficacy of threaded controls, finds the drawbacks of threaded control under production of high mix of semiconductors and suggests extensions and alternatives to improve threaded control. To evaluate the performance of threaded control, extensive simulations were performed in MATLAB. The effects of noise, disturbances, sampling and delays on the control and estimation performance of threaded controller were studied through these simulations. Based on the results obtained, several ideas to extend threaded control by reducing overall number of threads, by improving thread definitions and combination have been introduced. A unique idea of sampling the measurements dynamically based on the estimation accuracy is also presented. Future work includes implementing the extensions to threaded control suggested in this work in real production data and comparing the results without the use of those methods. Future work also includes building new alternatives to threaded control. / text