The sensor element of an imaging system should be mounted into its housing in such a way that the scene can be properly focused onto the sensor element's focal plane over the active area. Operational imaging requirements are forcing increasingly smaller tolerances on sensor alignment, and manufacturing systems must improve alignment capability to keep pace. Imaging system designs include reference datums that provide the basis for manufacturing alignment of optical components in each subassembly. Design constraints for alignment of the sensor element into the camera housing typically include x,y,z, clocking, and parallelism specifications. Measurement of z and parallelism positioning is often problematic, since the relevant reference datum features are often beneath the mounting platform and are obscured to the measurement system. General algorithms for determining sensor chip alignment when datum features are inaccessible to the measurement system are described. Precharacterization measurements of datum surfaces are used to determine datum locations during alignment measurement. The algorithms are useful for active manufacturing alignment as well as postmounting alignment measurement. The algorithms are successfully implemented for ultraprecision, active manufacturing alignment, and postalignment measurement of IR imaging systems.