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We have developed a code to reconstruct the Cosmic Rays trajectory in the Earth magnetosphere. This code solves the Lorentz equation and propagates a particle backward in time. The total magnetic field is evaluated by using the International Geomagnetic Reference Field (IGRF) 2000-2005 and the external magnetic field Tsyganenko-96. This code has been used both for a simulation of randomly generated inputs and for the analysis of the AMS-01 experiment data taken during the STS-91 Space Shuttle mission in June 1998. By a full spectrum simulation we have separated the primary Cosmic Ray component from the secondary one present at the altitude of AMS orbit (400 km). We have built the transmission function in the magnetosphere for 1998 for several regions with different geomagnetic latitude. The same simulation has also been performed for the magnetic conditions of the year 2005, the expected starting time of the long-duration AMS-02 data taking. Then we have estimated the variation of the transmission function with time and obtained the primary Cosmic Ray flux at the altitude of 400 km starting from the flux at 1 AU as predicted by the CREME96 model. more...