A second stage screening system configured to resolve a threat alarm detected in a cargo by a first stage screening system. The second stage screening system includes layers of first muon detectors placed above the cargo to detect a first coordinate and an angle of incidence of incoming muons and layers of second muon detectors placed below the cargo to detect an actual coordinate and an actual angle of exit of the incoming muons. The first and second detectors measure a momentum of the incoming muons. A processing unit receives threat sensitivity vectors determined from the first stage, operates a cargo positioning system that centers a high-Z threat within the cargo, relative to the first and second muon detectors, and analyzes the momentum and a distribution of deflection angles between the angles of incidence and exit to resolve the threat alarm.