A system and method for baggage screening at security checkpoints. A CT scanner system processes x-ray data to locate and eliminate non-contraband without a full CT reconstruction of the entire bag. The CT scanner system utilizes lineogram data to disqualify objects of insufficient size, density, or mass as potential threats. Objects can be inspected with CT reconstruction. The CT scanner is capable of obtaining CT data and projection images. Multiple CT scanning systems can be multiplexed together, and each CT scanning system is in communication with a review station. Baggage scanning may also be based on security intelligence inputs such as CAPPS to increase throughput.