A system for containing and transporting a medical device may include a container including a bottom face and surrounding side faces as a closed first end and an open second end to form an inner portion for receiving and retaining the medical device. The liner may be extendable over the side faces to line the inner portion of the container to an outer surface of the bottom face of the container. The liner may act as a protective barrier to the container to minimize contamination when receiving and/or retaining a used medical device. First and second covers may be removably attachable to the container, over the liner, to enclose a medical device therebetween. A first cover may have a color or marking indicating the medical device is “clean”, while a second cover may have a color or marking indicating the medical device is “used”.