This specification is directed towards finding, locating, and confirming threat items and substances. The inspection system is designed to detect objects that are made from, but not limited to, special nuclear materials (“SNM”) and/or high atomic number materials. The system employs a dual energy CT scanning first stage inspection system and advanced image processing techniques to analyze images of an object under inspection (“OUI”), which includes, but is not limited to baggage, parcels, vehicles and cargo.