The CT threat resolution system includes an primary EDS scanning process to identify threats and the nature of threats and a plurality of secondary CT scanning processes to resolve threats. The primary EDS scanning process and secondary CT scanning processes can be either separate machines or multiple processes within a single scanner. The secondary scanning process may utilizes dual energy scanning and/or high resolution scanning to resolve threats based upon the nature of the threat. An alarm indicates threats which cannot be resolved by the secondary CT scanning process for further operator investigation. Threats may be reviewed and resolved by an operator before the secondary CT scanning process.