Semiconducting materials require stringent design specifications that make their fabrication more difficult and prone to flaws that are costly and damaging to their computing and electrical properties. Area-selective atomic layer deposition is a process that addresses concerns associated with design imperfections but requires substantial monitoring to ensure that process regulation is maintained. This work proposes a run-to-run controller with an exponentially weighted moving average method for an area-selective atomic layer deposition rotary reactor by adjusting the rotation speed of the substrate to control the growth per cycle of the wafer, which is calculated through a multiscale model with machine learning integration for pressure field generation and kinetic Monte Carlo simulations to increase computational efficiency. Results indicate that the run-to-run controller was able to bring the process to the setpoint when subjected to moderate pressure and kinetic shift disturbances.