Shims used to join part assemblies are automatically designed and fabricated without the need for fitting part assemblies together in order to determine the exact dimensions of voids filled by the shims. The locations of key features on part assemblies are surveyed using a merged photogrammetry and laser tracking technique that generate the dimensions of a virtual shim. The dimensions of the virtual shim are contained in a digital file that can be used to automatically fabricate the shim using automated fabrication equipment such as a CNC machining center. The automated virtual shim design may be modified to reflect the effect of part assembly fit on performance characteristics of the aircraft.