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A project was launched to improve Shallow Trench Isolation (STI) etch depth control on magnetically enhanced reactive ion etch (MERIE) chambers. The aim was to reduce the wafer-to-wafer depth variation. The cause of the wafer-to-wafer depth variation was found to be due to a number of factors, including: (a) Multiple chamber/platform of film deposition tools, (b) Multiple Film Thickness Metrology tools, (c) Multiple etch chamber/platform tools and (d) Multiple STI Depth metrology equipment. To account for these variations, a feedback Run-to-Run control loop has been developed. The algorithm utilizes pre-etch film thickness and post-etch STI depth metrology data to output a new etch time for a particular chamber in order to re-center the process. The challenges that where overcome with the Run-to-Run (R2R) algorithm included: (1) Filtering incoming data from possible "flyers," (2) Accounting for uncertainties associated with different metrology tools and (3) Improving the robustness of the control algorithm. After implementation, in-silicon depth standard deviation was reduced to ∼1/3 of its original value. SPC (statistical process control) parameters were also significantly improved.