Methods and apparatus that introduce, within the ion implant chamber or an isolated chamber in communication therewith, the capability to remove contaminants and oxide surface layers on a wafer surface prior to ion implantation, are disclosed. The mechanisms for removal of contaminants include conducting: a low energy plasma etch, heating the wafer and application of ultraviolet illumination, either in combination or individually. As a result, implantation can occur immediately after the cleaning/preparation process without the contamination potential of exposure of the wafer to an external environment. The preparation allows for the removal of surface contaminants, such as water vapor, organic materials and surface oxides.