Polymeric microfluidic bioreactor arrays have high potentials in the use of low-cost disposable diagnostic and analytical devices due to the unique advantages of small reagent consumption and highly parallel experimentation capability. However, at micrometer scale, capillary effect plays a prominent role in liquid flow at the startup phase, especially creating problems in filling multiple hydrophobic channels and wells with abruptly changing boundaries from one common inlet. This problem may even occur in just two parallel poly(dimethylsiloxane) (PDMS) microchannels fabricated with multi-layer soft lithography. This work investigates this phenomenon. Theoretical studies based on microfluidic models for pressure drop showed that uniform flow can be achieved with properly designed geometries and dimensions for microchannels and/or by surface modification. By filling the microwells with fibrous matrices to increase flow resistance and balance capillary pressures, uniform flow distribution among parallel microchannels and wells was achieved. The result from this work demonstrated the importance of material selection, design and process for fabricating microfluidic devices. A uniform microfluidic flow in the microbioreactor array is critical to flow-through high-throughput experimentations for drug screening and cell culture process optimization.