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This work focuses on modeling and control of aggregate thin film surface morphology for improved light trapping using a patterned deposition rate profile. The dynamics of the evolution of the thin film surface height profile are modeled by an Edwards-Wilkinson-type equation (a second-order stochastic partial differential equation) in two spatial dimensions. The thin film surface morphology is characterized in terms of aggregate surface roughness and surface slope. These variables are computed with respect to appropriate visible light-relevant characteristic length scales and defined as the root-mean-squares of height deviation and slope of aggregate surface height profiles, respectively. Analytical solutions of the expected aggregate surface roughness and surface slope are obtained by solving the Edwards-Wilkinson equation and are used in the controller design. The model parameters of the Edwards-Wilkinson equation can be estimated from kinetic Monte-Carlo simulations using a novel parameter estimation procedure. This parameter dependence on the deposition rate is used in the formulation of the predictive controller to predict the influence of the control action on the surface roughness and slope at the end of the growth process. The cost function of the controller involves penalties on both aggregate surface roughness and mean slope from set-point values as well as constraints on the magnitude and rate of change of the control action. The controller is applied to the two-dimensional Edwards-Wilkinson equation. Simulation results show that the proposed controller successfully regulates aggregate surface roughness and slope to set-point values at the end of the deposition that yield desired levels of thin film reflectance and transmittance levels.