The ability to pattern porous materials with functional polymeric coatings is important for the fabrication of next-generation microfluidic platforms, membranes, tissue scaffolds, and optical devices. Here, we demonstrate for the first time that solventless initiated chemical vapor deposition (iCVD) can be used for three-dimensional patterning of porous substrates. The individual fibers of hydrophilic chromatography paper were uniformly coated with a thin layer of hydrophobic photoresponsive poly(o-nitrobenzyl methacrylate) (PoNBMA). X-Ray photoelectron spectroscopy and contact angle measurements confirmed that the PoNBMA coating penetrated the entire depth of the paper and scanning electron microscope images confirmed that the porosity and hierarchical structure of the paper were retained during the coating process. The PoNBMA coating was then patterned through the entire depth of the paper by exposure to ultraviolet light followed by rinsing in biologically compatible buffer. We demonstrated the utility of our patterning process by fabricating three-dimensional hydrophilic and hydrophobic regions into the chromatography paper for use as paper-based microfluidic devices. Our patterning process represents an environmentally friendly method to pattern three-dimensional materials since no organic solvents are used during the polymerization process or patterning step.