A method of processing a substrate having horizontal and non-horizontal surfaces is disclosed. The substrate is implanted with particles using an ion implanter. During the ion implant, due to the nature of the implant process, a film may be deposited on the surfaces, wherein the thickness of this film is thicker on the horizontal surfaces. The presences of this film may adversely alter the properties of the substrate. To rectify this, a second process step is performed to remove the film deposited on the horizontal surfaces. In some embodiments, an etching process is used to remove this film. In some embodiments, a material modifying step is used to change the composition of the material comprising the film. This material modifying step may be instead of, or in addition to the etching process.