We prepared water dispersions of poly(n-butyl methacrylate-st-butyl acrylate) crosslinked core-shell nanoparticles functionalized with different amounts of trimethoxisilane (TMS) groups in the outer shell. The purpose of the TMS groups is to chemically bind the rubbery particles to a nanostructured silica network, using sol-gel copolymerization. Here, we present nanoparticles containing 13 mol % and 30 mol % of TMS groups in the outer shell and compare their surface morphology with particles that do not contain TMS. The particles are prepared by a two-step seeded emulsion polymerization technique at neutral pH. In the first step, we obtained crosslinked seed particles (44 nm in diameter) by a batch process. In the second step, we used a semi-continuous emulsion polymerization technique under starved feed conditions to obtain monodispersed particles of controlled composition and size (ca. 100 nm in diameter). Fluorescence decay measurements were performed in situ on the dispersions, using a pair of cationic dyes adsorbed onto the surface of the nanoparticles: rhodamine 6G as the energy transfer donor and malachite green carbinol hydrochloride as the acceptor. The kinetics of Förster resonance energy transfer (FRET) between the dyes is sensitive to the donor-acceptor distance, allowing us to obtain the binding distribution of the dyes at the nanoparticle surface. For the unmodified nanoparticles, we found a dye distribution that corresponds to an average interface thickness of delta = (5.2 +/- 0.2) nm. For the samples containing 13 mol % and 30 mol % of TMS groups in the outer shell we obtained broader interfaces, with widths of delta = (6.2 +/- 0.2) nm and delta = (6.5 +/- 0.1) nm respectively. This broadening of the distribution with the surface modification is interpreted in terms of the increase in free volume of the shell caused by the TMS groups. Finally, we studied the effect of temperature on the water-polymer interface fuzziness, in order to evaluate the accessibility of the TMS groups during the sol-gel synthesis of nanostructured hybrid materials.