The invention provides three methods for treating a fluorinated surface, which is a non-negligible problem of the interior of an ion implanter, and may become more serious when a low-energy fluorine-containing ion beam is implanted to a carbon surface and/or a silicon surface. Firsty, hydrogen and/or hydrogen-containing ions (atomic and/or molecular) is introduced to the fluorine-containing surface, so that the fluorine bond is replaced by the hydrogen bond, and then the fluorine-containing particles are removed. Secondly, a boron ion beam (especially a boron ion beam with a clean formula) isimplanted onto the fluorinated surface, so that the fluorine-containing particles are removed. Thirdly, the temperature of the fluorinated surface is adjusted, generally is heated, to a temperature range, so that the fluorine bonding is weakened and the fluorine-containing particles are easily volatilized and removed. Optionally, the fluorine-containing particles can be continuously, alternativelyor flexibly removed in a vacuumizing manner.