Scattering techniques with neutrons and X-rays are powerful methods for the investigation of the hierarchical structure of reinforcing fillers in rubber matrices. However, when using only X-ray scattering, the independent determination of the filler response itself sometimes remains an issue because of a strong parasitic contribution of the ZnO catalyst and activator in the vulcanization process. Microscopic characterization of filler-rubber mixtures even with only catalytic amounts of ZnO is, therefore, inevitably complex. Here, we present a study of silica aggregates dispersed in an SBR rubber in the presence of the catalyst and show that accurate partial structure factors of both components can be determined separately from the combination of the two scattering probes, neutrons, and X-rays. A unique separation of the silica filler scattering function devoid of parasitic catalyst scattering becomes possible. From the combined analysis, the catalyst contribution is determined as well and results to be prominent in the correction scheme. The experimental nano-structure of the ZnO after the mixing process as the by-product of the scattering decomposition was found also to be affected by the presence or absence of silica in the rubber mixture, correlated with the shear forces in the mixing and milling processes during sample preparation. The presented method is well suited for studies of novel dual filler systems.