Sequential deposition of nanofibrous Composites of charged perylene diimide (PI)I) dyes and Oppositely charged polyelectrolyte (PE) is demonstrated within fluidic devices. The PDIs employed include an amphiphilic, singly charged PDI (C7OPDI+) and a doubly charged species (TAPDI(2+)). Anionic poly(acrylate) (PA(-), 5100 and 250K MW) is used as the PE. As previously demonstrated [Weitzel, C. R.; Everett, T. A.; Higgins, D. A. Langmuir. 2009, 25 1188], dip-coated PDI/PE composites form nanofibrous films that exhibit flow-induced alignment clue to gravitational draining of the dipping solution. In this study, the potential for producing patterned, flow-aligned PD/PE composites by deposition using pressure-driven flow within fluidic channels is explored. The influence of flow profile, PE molecular weight (MW) and PD1 structure oil deposition efficiency, macroscopic and microscopic morphology, and the potential for nanofiber alignment are also investigated. Optical absorbance microscopy and tapping mode AFM data demonstrate that C7OPDI+/PA(-) deposition is controlled by PDI aggregation, while TAPDI(2+)/PA(-) composites are more dependent upon PE MW. Optical dichroism images show that C7OPDI+/PA(-) composites form serpentine, partially aligned nanofibers under all conditions explored, while TAPDI(2+)/PA(-) films incorporate more tightly packed nanofibers that form randomly oriented nematic-like domains when high MW PA(-) is employed. In-plane organization in C7OPDI+/ PA(-) films is concluded to result from flow-induced alignment of solution-formed C7OPDI+ aggregates, while the unaligned domains found in TAPDI(2+)/PA(-) films are concluded to form on the substrate surface by the complexation of small TAPDI(2+) aggregates or monomers with PE.