In this work, we focus on the development of a multiscale modeling and run-to-run control framework with the purpose of improving thin film product quality in a batch-to-batch plasma-enhanced chemical vapor deposition (PECVD) manufacturing process. Specifically, at the macroscopic scale, gas-phase reaction and transport phenomena yield deposition rate profiles across the wafer surface which are then provided to the microscopic domain simulator in which the complex microscopic surface interactions that lead to film growth are described using a hybrid kinetic Monte Carlo algorithm. Batch-to-batch variability has prompted the development of an additional simulation layer in which an exponentially weighted moving average (EWMA) control algorithm operates between serial batch deposition sequences to adjust the operating temperature of the PECVD reactor to overcome drift in the electron density of the plasma. Application of the run-to-run (R2R) control system developed here is shown to reduce offset in the product thickness from 5% to less than 1% within 10 batches of reactor operation. Finally, we propose an extension of the EWMA algorithm to four independent, radial wafer zones in order to improve thickness uniformity in the presence of spatially non-uniform species concentrations. It is demonstrated that the produced thin films can be driven to the desired thickness set-point of 300 nm in less than 10 batches in the presence of both electron density drift and non-uniform deposition rate profiles. (C) 2016 Elsevier Ltd. All rights reserved.