- As muons come from the sky, they pass through the top detector, the truck and the bottom detector. The muons create ionization trails in the scanner's gas-filled detector tubes, which sensors record.
- Heavy atoms, such as uranium and plutonium, deflect muons more than lighter ones do. If the angles of muons' entrance and exit paths vary by a wide magin, nuclear material could be present.
- The detector also senses gamma radiation, which the computer combines with muon data to build a 3D view of suspicious muon-scattering objects, alerting customs agents exactly where to search.