A coating is applied to a work piece in a charged particle beam system without directing the beam to work piece. The coating is applied by sputtering, either within the charged particle beam vacuum chamber or outside the charged particle beam vacuum chamber. In one embodiment, the sputtering is performed by directing the charged particle beam to a sputter material source, such as a needle from a gas injection system. Material is sputtered from the sputter material source onto the work piece to form, for example, a protective or conductive coating, without requiring the beam to be directed to the work piece, thereby reducing or eliminating damage to the work piece.