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In this work, we develop a method for dynamic output feedback covariance control of the state covariance of linear dissipative stochastic partial differential equations (PDEs) using spatially distributed control actuation and sensing with noise. Such stochastic PDEs arise naturally in the modeling of surface height profile evolution in thin film growth and sputtering processes. We begin with the formulation of the stochastic PDE into a system of infinite stochastic ordinary differential equations (ODEs) by using modal decomposition. A finite-dimensional approximation is then obtained to capture the dominant mode contribution to the surface roughness profile (i.e., the covariance of the surface height profile). Subsequently, a state feedback controller and a Kalman-Bucy filter are designed on the basis of the finite-dimensional approximation. The dynamic output feedback covariance controller is subsequently obtained by combining the state feedback controller and the state estimator. The steady-state expected surface covariance under the dynamic output feedback controller is then estimated on the basis of the closed-loop finite-dimensional system. An analysis is performed to obtain a theoretical estimate of the expected surface covariance of the closed-loop infinite- dimensional system. Applications of the linear dynamic output feedback controller to the linearized stochastic Kuramoto- Sivashinsky equation are presented.