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The flow conditions in a parallel plate "bioreactor" have been modeled using computational fluid dynamics (CFD) and characterized experimentally using a computer controlled flow regulation apparatus and associated flow visualization techniques. The conditions required to induce flow characteristics appropriate for standard in-vitro cell processes on flat substrates have been identified from a consideration of data from previous studies. The effects of changing the surface topography of the substrate on which the cells are grown has been investigated by forming specific micrometer scale features via hot embossing on polymeric plates. The effect that various features have on the flow that occurs at the boundary layer adjacent to the surface in the parallel plate chamber has been determined. The results for studies undertaken in a parallel plate chamber operating under computer control are presented here. Flow characteristics have been determined using feedback from the sensors within the system and validated by direct flow visualization using fluorescent beads and modeled using a CFD routine. The system exhibits well developed laminar flow and is capable of delivering surface shear stresses up to 2.4 Pa on a planar surface. As such, it is suitable for evaluating in-vitro cell processes. The effects that the features produced by hot embossing of a poly methyl methacrylate (PMMA) surface have been tested in the flow chamber and their influence on shear stress observed.