A method for passivating a surface of a semiconductor substrate with fluorine-based layer to protect the surface against oxidation and allow longer queue times. According to one embodiment, the method includes providing a substrate having an oxidized layer formed thereon, replacing the oxidized layer with a fluorine-based layer, exposing the fluorine-based layer to an oxidizing atmosphere, where the fluorine-based layer protects the substrate against oxidation by the oxidizing atmosphere, and removing the fluorine-based layer from the substrate using a plasma process. According to another embodiment, the method includes providing a passivated substrate in a vacuum processing tool, the passivated substrate having a fluorine-based layer thereon that is effective for protecting the passivated substrate against oxidation by an oxidizing atmosphere, removing the fluorine-based layer from the passivated substrate using a microwave plasma process in the vacuum processing tool, thereby forming a clean substrate, and processing the clean substrate under vacuum conditions.