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Monte Carlo methods are increasingly considered powerful tools for accurate calculations of dose deposition, since they are assumed to provide a more realistic representation of the physical interactions undergone by the primary beam and the resulting secondaries. In this work, we briefly outline the use of the FLUKA Monte Carlo code for hadron therapy applications starting from the possibility of generating physical databases to be input into analytical treatment planning systems. In addition, we present the main features of our customization of FLUKA for CT (computed tomography) - based calculations of physical and biological effective dose delivery for the GSI actively shaped treatment fields in carbon ion therapy. Biological effective dose distributions are computed interfacing FLUKA with the GSI biophysical Local Effect Model.