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This paper deals with finite-dimensional boundary control of the two-dimensional (2-D) flow between two infinite parallel planes. Surface transpiration along a few regularly spaced sections of the bottom wall is used to control the flow. Measurements from several discrete, suitably placed shear-stress sensors provide the feedback. Unlike other studies in this area, the flow is not assumed to be periodic, and spatially growing flows are considered. Using spatial discretization in the streamwise direction, frequency responses for a relevant part of the channel are obtained. A low-order model is fitted to these data and the modeling uncertainty is estimated. An H∞ controller is designed to guarantee stability for the model set and to reduce the wall-shear stress at the channel wall. A nonlinear Navier-Stokes PDE solver was used to test the designs in the loop. The only assumption made in these simulations is that the flow is two dimensional. The results showed that, although the problem was linearized when designing the controller, the controller could significantly reduce fundamental 2-D disturbances in practice.