The specific self-assembly of Si/SiOx core-shell nanoparticles onto UV/ozone micropatterned poly(dimethylsiloxane) (PDMS) films is reported here. Auger and Raman spectroscopic mapping document the preferential Sii SiOx nanoparticle adsorption within PDMS domains (see Figure). These nanoparticles display a high refractive index, which renders them potentially important for photonic bandgap applications.