The use of three-dimensional (3D) models for education, pre-operative assessment, presurgical planning, and measurement have become more prevalent. With the increase in prevalence of 3D models there has also been an increase in 3D reconstructive software programs that are used to create these models. These software programs differ in reconstruction concepts, operating system requirements, user features, cost, and no one program has emerged as the standard. The purpose of this study was to conduct a systematic comparison of three widely available 3D reconstructive software programs, Amira®, OsiriX, and Mimics®, with respect to the software's ability to be used in two broad themes: morphometric research and education to translate morphological knowledge. Cost, system requirements, and inherent features of each program were compared. A novel concept selection tool, a decision matrix, was used to objectify comparisons of usability of the interface, quality of the output, and efficiency of the tools. Findings indicate that Mimics was the best-suited program for construction of 3D anatomical models and morphometric analysis, but for creating a learning tool the results were less clear. OsiriX was very user-friendly; however, it had limited capabilities. Conversely, although Amira had endless potential and could create complex dynamic videos, it had a challenging interface. These results provide a resource for morphometric researchers and educators to assist the selection of appropriate reconstruction programs when starting a new 3D modeling project.