The present specification discloses methods for inspecting an object. The method includes scanning an object in a two-step process. In the primary scan, a truck or cargo container (container) is completely scanned with a fan beam radiation, the transmitted radiation is measured with an array of detectors, and the transmission information and optionally the fission signatures are analyzed to determine the presence of high-density, high-Z and fissionable materials. If the container alarms in one or more areas, the areas are subjected to a secondary scan. This is done by precisely repositioning the container to the location of the suspect areas, adjusting the scanning system to focus on the suspect areas, performing a stationary irradiation of the areas, and analyzing the measured feature signatures to clear or confirm the presence of SNM.