This invention discloses an ion implantation apparatus with multiple operating modes. It has an ion source and an ion extraction means for extracting a ribbon-shaped ion beam therefrom. The ion implantation apparatus includes a magnetic analyzer for selecting ions with specific mass-to-charge ratio to pass through a mass slit to project onto a substrate. Multipole lenses are provided to control beam uniformity and collimation. The invention further discloses a two-path beamline in which a second path incorporates a deceleration system incorporating energy filtering. The invention discloses methods of ion implantation in which the mode of implantation may be switched from one-dimensional scanning of the target to two-dimensional scanning, and from a simple path to an s-shaped path with deceleration.