The substrate in a plasma jet deposition system is provided with structural attributes, such as apertures and/or grooves, that facilitate efficient deposition. Groups of substrates are arranged with respect to the plasma beam in a manner which also facilitates efficient deposition. In addition to increasing the portion of the plasma beam volume which contacts the substrate surface or surfaces, it is advantageous to provide for the efficient evacuation of spent fluids away from the substrate so that fresh plasma containing the operative species can easily and continuously contact the substrate surface.