A systematic computational fluid dynamics (CFD) approach has been applied to design the geometry of the channels of a three-dimensional (thick-walled) screen comprising upstream and downstream sets of elongated channels positioned at an angle of 90° with respect to each other. Such a geometry of the thick-wall screen can effectively drop the ratio of the maximum flow velocity to mean flow velocity below 1.005 in a downstream microstructured reactor at low Reynolds numbers. In this approach the problem of flow equalization reduces to that of flow equalization in the first and second downstream channels of the thick-walled screen. In turn, this requires flow equalization in the corresponding cross-sections of the upstream channels. The validity of the proposed design method was assessed through a case study. The effect of different design parameters on the flow non-uniformity in the downstream channels has been established. The design equation is proposed to calculate the optimum values of the screen parameters. The CFD results on flow distribution were experimentally validated by Laser Doppler Anemometry measurements in the range of Reynolds numbers from 6 to 113. The measured flow non-uniformity in the separate reactor channels was below 2%.