Systems and methods are provided for removing air from a medical device, such as a stent-graft and/or its delivery device. In an exemplary embodiment, the stent-graft or its delivery system or both are exposed to perfluorocarbon, by immersing the stent-graft or flushing the delivery device to remove air from the stent-graft. Optionally, the stent-graft and/or delivery system may be flushed multiple times, e.g., with perfluorocarbon before or after flushing with carbon dioxide, saline, a bio-inert gas, and the like. Thereafter, the stent-graft may be introduced into a patient's body and deployed at a target location, such as the site of an abdominal aortic aneurysm.