Methods of cleaning a medical device are provided via exposing the medical device to a compressed CO2-based mixture. The compressed CO2-based mixture includes carbon dioxide, a surfactant, and water in the form of water-in-CO2 microemulsions. In one particular embodiment, the ratio of water-to-surfactant mixed together in the CO2 has a range of about 5-100 molecules of water per molecule of surfactant (e.g., about 5-30 molecules of water per molecule of surfactant).