Methods and systems for scanning a container for contraband are provided. In one aspect, a method includes scanning the container using computed tomography (CT) to identify a location of an item of interest, determining a nuclear resonance fluorescence (NRF) scan configuration based on the location of the item of interest, positioning the container in the NRF scan configuration, irradiating the item of interest, detecting gamma rays emitted from the item of interest to generate signals representative of the detected gamma rays, and analyzing the generated signals to determine a presence of contraband.