For evaluating the contents of trucks, containers, cargo, and passenger vehicles by a non-intrusive gamma-ray or X-ray imaging system to determine the possible presence of contraband, three-dimensional (3D) measurements could provide more information than 2D measurements. In this paper, a linear pushbroom scanning model is built for such a commonly used gamma-ray or x-ray cargo inspection system. Accurate 3D measurements of the objects inside a cargo can be obtained by using two such scanning systems with different scanning angles to construct a pushbroom stereo system. A simple but robust calibration method is proposed to find the important parameters of the linear pushbroom sensors. Then, a fast and automated stereo matching algorithm based on free-form deformable registration is developed to obtain 3D measurements of the objects under inspection. A user interface is designed for 3D visualization of the objects in interests. Experimental results of sensor calibration, stereo matchin...