Optical designs for the next generation space science instruments call for unconventional, aspheric, and freeform (FF), prescriptions with tight tolerances. These advanced surfaces enable superior-performance, compact, and lower cost systems but are more challenging to characterize and, hence, to fabricate and integrate. A method was developed to characterize a wide range of optical surfaces, without requiring custom-made correctors, and to align them to each other for a high-performance optical system. A precision coordinate measuring machine, equipped with a non-contact, chromatic confocal probe, was used to measure numerous optics including large convex conics, high-sloped aspherics, several FF surfaces, and grazing-incidence x-ray optics. The resulting data were successfully reduced using custom-developed, advanced surface fitting analysis tool, to determine the optic’s alignment relative to the global and local coordinate systems, surface departure from design, and the as-built optical prescription. This information guided the modeling and the alignment of the corresponding as-built optical systems, including a flight system composed of a three-mirror anastigmat.