Organic-inorganic hybrid nanoparticles, derived from silica precursors with different organic functionalities (methyl, ethyl, vinyl, and phenyl) synthesized via a modified Stöber method have been investigated. These particles are intended as modifiers for polymers and polymer matrix composites. Therefore, the characteristics of a polyester matrix have also been determined, and the likely interactions with the particles have been proposed. Particles have been characterized using inverse gas chromatography (IGC), X-ray photoelectron spectroscopy (XPS), and infrared spectroscopy (FT-IR). The particles show two different sets of characteristics, with methyl, ethyl, and vinyl modified silicas showing one type of behavior and the phenyl modified silica behaving rather differently. The methyl, ethyl, and vinyl groups exhibit the appearance of uniform coverage, as they are comparatively small and tightly packed, which will prevent interaction of matrix resin with retained silanol groups. The phenyl group, which is comparatively large, is not able to pack as closely, which results in a reduction of the presence and availability of silanol groups, compared to an unmodified fumed silica, but not complete inaccessibility as far as the matrix resin is concerned.