Using computational modeling, we simulate the 3D movement of actuated cilia in a fluid-filled microchannel. The cilia are modeled as deformable, elastic filaments, and the simulations capture the complex fluid-structure interactions among these filaments, the channel walls, and the surrounding solution. The cilia are tilted with respect to the surface and are actuated by a sinusoidal force that is applied at the free ends. We find that these cilia give rise to a unidirectional flow in the system and by simply altering the frequency of the applied force we can controllably switch the direction of the net flow. The findings indicate that beating, synthetic cilia could be harnessed to regulate the fluid streams in microfluidic devices.