We describe a scalable synthesis process for the production and patterning of polymer matrix nanocomposites (PMNCs) using femtosecond laser irradiation to target specific functional behaviors. A modified, in situ chemical vapor deposition (CVD), nanoinfusion process was used to nucleate and grow nanoparticles in the bulk of an optically transparent polytetrafluoroethylene-co-hexafluoropropylene (FEP) polymer matrix. Metallic nanoparticles synthesized with this process can have a strong optical absorption at their surface plasmon resonance (SPR) frequency and we have utilized this property to selectively irradiate and pattern nanocomposites via femtosecond, photothermal heating. If the nanoparticle environment includes species used for chemical vapor deposition, the heat causes a localized decomposition of the precursor species in the immediate vicinity of the nanoparticle leading to a variety of core-shell nanostructures. Using this processing scheme, we have grown shells of tungsten oxide around silver nanoparticles within the polymer matrix resulting in a 40 nm red shift in the SPR of the silver nanoparticles in regions of the material exposed to femtosecond laser pulses. This process has also been adapted to polymers containing tungsten oxide nanoparticles so that the photocatalytic behavior of the particles could be used to the decompose precursor species in the immediate vicinity of the irradiated nanoparticles. These results demonstrate that, by using optical masks and laser processing, it is possible to synthesize nanocomposites with a high degree of control over the location, composition, size, and distribution of nanoparticles within a polymer matrix resulting in patterned materials with tailored electrical, optical, and photocatalytic properties.