Systems and methods that mitigate contamination and modify surface characteristics during ion implantation processes through the introduction of gases

A contamination mitigation or surface modification system for ion implantation processes includes a gas source, a controller, a valve, and process chamber. The gas source provides delivery of a gas, be it atmospheric or reactive, to the valve and is controlled by the controller. The valve is located on or about the process chamber and controllably adjusts flow rate and/or composition of the gas to the process chamber. The process chamber holds a target device, such as a target wafer and permits interaction of the gas with an ion beam to mitigate contamination of the target wafer and/or to modify the existing properties of the processing environment or target device to change a physical or chemical state or characteristic thereof. The controller selects and adjusts composition of the gas and flow rate according to contaminants present within the ion beam, or lack thereof, as well total or partial pressure analysis.