Atmospheric pressure discharges are routinely used to functionalize rough surfaces of commodity polymeric materials to enhance surface properties. High value polymeric materials, such as scaffolding for tissue engineering, must also have their surfaces treated to achieve similar functionality. The techniques used to achieve this functionality are typically costlier than the commodity processes used for bulk, web treatment of polymer sheets. The issue we are investigating is whether inexpensive, commodity plasma processes can be adapted to treat high value materials while considering the uniformity of processing on micro- and macro-scales. To address these issues a two-dimensional plasma hydrodynamics-surface kinetics model was developed and applied to the investigation of atmospheric pressure plasma functionalization of a polypropylene surface having microstructure using He/O₂/H₂O mixtures. Non-uniformities in functionalization occur over both macroscopic and microscopic length scales and can be controlled by a judicious choice of O₂ fraction.