The exact modeling of external and internal perturbations acting on spacecraft becomes increasingly important as the scientific requirements become more demanding. Disturbance models included in orbit determination and propagation tools need to be improved to account for the needed accuracy. At ZARM (Center of Applied Space Technology and Microgravity) algorithms for the simulation and analysis of thermal perturbations have been developed. The applied methods are based on the inclusion of the actual spacecraft geometry by means of Finite Element (FE) models in the calculation of the disturbance forces. Thus the modeling accuracy is increased considerably and also housekeeping and sensor data can be included in the calculations. Preliminary results for a test case geometry of the Pioneer 10/11 mission are presented and discussed with respect to the Pioneer anomaly. It is shown that thermal effects cannot be neglected for the magnitude scale of the observed anomalous effect.