Recently it has become clear that the magnetic filter field used in the JET NBI Ion Source, to enhance the monatomic species yield, also produces non-uniformity in the ion density, which causes reduced transmission of the extracted beam. A Monte-Carlo model has been developed to trace the trajectories of electrons and ions through the three dimensional magnetic field of the ion source. This model has reproduced the measured non-uniformity of the filter field ion source. Use of this Monte-Carlo model has assisted the development of a high monatomic yield ion source with improved plasma uniformity.