This work focuses on model parameter estimation and model-based output feedback control of surface roughness in a sputtering process which involves two surface micro-processes: atom erosion and surface diffusion. This sputtering process is simulated using a kinetic Monte Carlo (kMC) simulation method and its surface height evolution can be adequately described by the stochastic Kuramoto-Sivashinsky equation (KSE), a fourth-order nonlinear stochastic partial differential equation (PDE). First, we estimate the four parameters of the stochastic KSE so that the expected surface roughness profile predicted by the stochastic KSE is close (in a least-square sense) to the profile of the kMC simulation of the same process. To perform this model parameter estimation task, we initially formulate the nonlinear stochastic KSE into a system of infinite nonlinear stochastic ordinary differential equations (ODEs). A finite-dimensional approximation of the stochastic KSE is then constructed that captures the dominant mode contribution to the state and the evolution of the state covariance of the stochastic ODE system is derived. Then, a kMC simulator is used to generate representative surface snapshots during process evolution to obtain values of the state vector of the stochastic ODE system. Subsequently, the state covariance of the stochastic ODE system that corresponds to the sputtering process is computed based on the kMC simulation results. Finally, the model parameters of the nonlinear stochastic KSE are obtained by using least-squares fitting so that the state covariance computed from the stochastic KSE process model matches that computed from kMC simulations. Subsequently, we use appropriate finite-dimensional approximations of the identified stochastic KSE model to design state and output feedback controllers, which are applied to the kMC model of the sputtering process. Extensive closed-loop system simulations demonstrate that the controllers reduce the expected surface roughness by 55% compared to the corresponding values under open-loop operation. (C) 2007 Elsevier Ltd. All rights reserved.