Using finite-element analysis (FEA) to numerically mount compliant components onto their inspection fixture is an approach proposed by researchers in the field of computational metrology. To address the shortcomings of the underlying principle of current methods, this paper presents a boundary displacement constrained (BDC) optimization using FEA. The optimization seeks to minimize the distance between corresponding points, in the scanned manufactured part and the nominal model, that are in unconstrained regions. This is done while maintaining that a distance between corresponding points in constrained regions (i.e., fixing points) remains within a specified contact distance. At the same time, the optimization limits the magnitude and direction of forces on boundary. In contrast to the current methods, postprocessing of the point cloud is not required since the method uses information retrieved from the FEA of the nominal model to estimate the manufactured part’s mechanical behavior. To investigate the performance of the proposed method, it is tested on ten (10) free-state simulated manufactured aerospace panels that differ in their level of induced deformation. Results are then compared to those obtained using the underlying principles of current methods.