Current methods to discretize the interior morphology of unreinforced masonry structures for computational modelling are limited to simplification and gross estimation of the true morphology. Digital recording methods are capable of efficiently capturing geometric and colour information of structures’ surface topography with metric accuracy at a high level of detail, and with highly controllable precision. However, they are limited in detecting sub-surface conditions. Nondestructive testing methods offer tools to understand sub-surface conditions in masonry structures. Ultrasonic pulse velocity testing specifically is an established tool for detecting internal conditions in masonry and concrete structures, with potential for identifying metrically accurate geometric anomalies inside complex historic masonry assemblies. The integration of sub-surface imaging results from nondestructive testing with digital recording data has been limited to visualization for condition assessments. Using sub-surface imaging data to inform computational modelling offers a promising approach to increase the level of detail in the structural analysis of unreinforced masonry structures. This research presents the best practices and limitations for employing ultrasonic pulse velocity testing to generate tomographic reconstructions of unreinforced masonry assemblies. Ultrasonic testing is conducted on limestone and clay brick masonry units and multi-wythe assemblies to establish protocols for ultrasonic measurements and tomographic processing, and to define physical limitations of the tested masonry assemblies. The tomographic reconstruction results are integrated with photogrammetric data in preparation for generating a discontinuum-based computational model.