3D metrology techniques are disclosed for determining a changing topography of a substrate processed in an additive manufacturing system. Techniques include fringe scanning, simultaneous fringe projections, interferometry, and x-ray imaging. The techniques can be applied to 3D printing systems to enable rapid topographical measurements of a 3D printer powder bed, or other rapidly moving, nearly continuous surface to be tested. The techniques act in parallel to the system being measured to provide information about system operation and the topography of the product being processed. A tool is provided for achieving higher precision, increasing throughput, and reducing the cost of operation through early detection and diagnosis of operating problems and printing defects. These techniques work well with any powder bed 3D printing system, providing real-time metrology of the powder bed, the most recently printed layer, or both without reducing throughput.