We report on spatial control of nanoporosity in polyelectrolyte multilayer (PEM) films using photopatterning and its effects on film optical and adsorption properties. Multilayers assembled from poly(acrylic acid-ran-vinylbenzyl acrylate) (PAArVBA), a photo-cross-linking polymer, and poly(allylamine hydrochloric acid) (PAH) were patterned using ultraviolet light followed by immersion in low pH and then neutral pH solutions to induce nanoporosity in unexposed regions. Model charged small molecules rhodamine B, fluorescein, and propidium iodide and the model protein albumin exhibit increased adsorption to nanoporous regions of patterned PEM films as shown by fluorescence microscopy and radiolabeling experiments. Films assembled with alternating stacks of PAH/poly(sodium-4-styrene sulfonate) (SPS), which do not become nanoporous, and stacks of PAH/PAArVBA were patterned to create nanoporous capillary channels. Interdigitated channels demonstrated simultaneous, separate wicking of dimethyl sulfoxide-solvated fluorescein and rhodamine B. In addition, these heterostack structures exhibited patternable Bragg reflectivity of greater than 25% due to refractive index differences between the nanoporous and nonporous stacks. Finally, the PEM assembly process coupled with photo-cross-linking was used to create films with two separate stacked reflective patterns with a doubling in reflectivity where patterns overlapped. The combined adsorptive and reflective properties of these films hold promise for applications in diagnostic arrays and therapeutics delivery.