An atmospheric plasma treatment station is integrated in a semiconductor process tool. The atmospheric plasma treatment station directly interfaces with a deposition chamber of the semiconductor process tool without adding to the footprint or form factor of the semiconductor process tool. The atmospheric plasma treatment station includes a movable atmospheric plasma source such as a linear head for scanning across a surface of a substrate. The atmospheric plasma treatment station provides an enclosed space in a controlled environment with non-reactive gas flowing through the enclosed space. Process gases may be supplied to the linear head based on a surface condition of the substrate being treated.