Additive manufacturing components are prone to defects, including warping and cracking, which can significantly impact their mechanical performance. Determining deformations in lattice structures remains challenging. This paper presents a methodological framework for computing deformation matrices in additively manufactured lattice samples using 3D scanning. The sample’s geometry is acquired through 3D scanning, registered to a reference model, and vertices are determined and used for computing deformation metrics, including volumetric scaling factors, isovolumetric scaling, and angular deformations. A sensitivity analysis comparing four association criteria demonstrates the reliability of the Gaussian Best Fit Plane External. Assessing deformation in lattice structures can be useful for optimizing printing parameters and compensating for process-induced deformations. Future work will extend this methodology to evaluate deformations during post-processing and develop mesh morphing strategies for generating printing geometries.