Thermal modeling of complex systems faces the problems of an effective digitalization of the detailed geometry and properties of the system, calculation of the thermal flows and temperature maps, treatment of the thermal radiation including possible multiple reflections, inclusion of additional external influences, extraction of the radiation pressure from calculated surface data as well as computational effectiveness. In previous publications [1, 2] the solution to these problems have been outlined and a first application to the Pioneer spacecraft have been shown. Here we like to present the application of our thermal modeling to the Rosetta flyby anomaly as well as to the Pioneer anomaly. The analysis outlines that thermal recoil pressure is not the cause of the Rosetta flyby anomaly but likely resolves the anomalous acceleration observed for Pioneer 10.