This paper reports the implementation in three dimensions (3D) of diffusion models for low dose implanted dopants in silicon and the various numerical issues associated with it. In order to allow the end-users to choose between high accuracy or small calculation time, a conventional and 5-species diffusion models have been implemented in the 3D module DIFOX-3D belonging to the PROMPT plateform. By comparison with one and two-dimensional (1D and 2D) simulations performed with IMPACT-4, where calibrated models exist, the validity of this 3D models have been checked. Finally, the results obtained for a 3-dimensional simulation of a rapid thermal annealing step involved in the manufacturing of a MOS transistor are presented what show the capability of this module to handle the optimization of real devices.