Provided are methods and systems for aligning multiple parts using simultaneous scanning of features of different parts and using feature-based coordinate systems for determining relative positions of these. Specifically, a feature-based coordinate system may be constructed using one or more critical dimensions between features of different parts. The scanner may be specifically positioned to capture each of these critical dimensions precisely. The feature-based coordinate system is used to compare the critical dimensions to specified ranges. The position of at least one part may be adjusted based on results of this comparison using, for example, a robotic manipulator. The process may be repeated until all critical dimensions are within their specified ranges. In some embodiments, multiple sets of features from different parts are used such that each set uses its own feature-based coordinate system. The part adjustment may be performed based on the collective output from these multiple sets.