A system and method for magnetically filtering an ion beam during an ion implantation into a workpiece is provided, wherein ions are emitted from an ion source and accelerated the ions away from the ion source to form an ion beam. The ion beam is mass analyzed by a mass analyzer, wherein ions are selected. The ion beam is then decelerated via a decelerator once the ion beam is mass-analyzed, and the ion beam is further magnetically filtered the ion beam downstream of the deceleration. The magnetic filtering is provided by a quadrapole magnetic energy filter, wherein a magnetic field is formed for intercepting the ions in the ion beam exiting the decelerator to selectively filter undesirable ions and fast neutrals.