Removable barrier devices (e.g., sleeves) for covering medical scanning devices to reduce the chance of cross-contamination between patients and/or to protect the scanning devices from physical damage. The barrier device can include a cover that has an integrated window for passing optical signals between the scanning device and an external environment. The cover can include a sleeve that covers a handle portion of the scanning device to prevent contamination of the handle from a user's hand or glove. The cover and sleeve may both be formed of the same flexible material, or the cover may be rigid to maintain the window in a fixed position and the sleeve may be flexible to allow a user to activate a button or touchpad on the handle. An interface region between the cover and sleeve may provide a hermetic seal. The window may include a nanostructured antireflective material to limit internal reflections.