Semiconductor manufacturing employs an intricate framework of processes that require accurate design specifications at the nanoscale level. Thermal atomic layer etching fulfills these stringent criteria in an exemplary manner by conducting top-down removal of transistor films to further downsize thicknesses and facilitate transistor densification on wafers. However, it has low productivity. Thus, a spatial sheet-to-sheet reactor is appropriate for achieving high throughput while maintaining substrate quality. In order to continuously regulate the process, a run-to-run (R2R) controller coupled with a continuous feedback proportional–integral (PI) controller is proposed to mitigate a kinetic shift disturbance and a continuous pressure ramp disturbance through a multivariate input correction procedure. A tuning methodology is employed to determine the optimal tuning parameters to enhance the performance of the R2R and PI controller response to their respective disturbances. Results indicate that the combined R2R and PI controller outperforms the sole R2R controller by minimizing the amount of input correction needed to minimize the etching per cycle offset from the setpoint.