A multi-level contraband detection system. At a first level, the system obtains volumetric information about an item under inspection. The volumetric information provides a basis for identifying suspect objects in the item under inspection and their locations. The location information is expressed in a first coordinate system relative to the device used for first level scanning. When first level scanning identifies a suspicious object, the item under inspection is passed to a second level scanner that can take further measurements on the suspicious objects. The second level machine is controlled in a second coordinate system. A translation between the two coordinate systems is obtained by registering a multi-dimensional image obtained at the first level with positioning information obtained at the second level. Registration is performed using a coarse and then a fine registration process for quick and accurate registration.