Modern scanning methods have made anatomical digital reconstruction critical for assessing skeletal function. Hard tissues from the crania of 4 different species were used to assess digital reconstruction for accurately modeling relationships between shape and function. Digital information from humans, alligators, dogs, and rhesus monkeys were collected by using computed tomography scans. DICOM files were processed by using segmentation methods to separate tissues. Once hard tissue shapes were obtained, functional conditions were assigned to the morphology, and biomechanical characteristics were considered to evaluate the functional load effects. Three‐dimensional morphologies were obtained in every case. However, acquiring tissue separation was a challenging process affected by both the precision of data collection and experience with the software. Interestingly, biomechanical features, material properties, and physiological actions were very important in modeling function. The digital reconstruction of hard tissues is the first step to understanding the relationship between function and morphological features. But the process is incomplete without a comprehensive definition of functional actions, material, and biomechanical characteristics of the anatomical elements. Supported by NSF BCS 0725126, NIH/NIDCR DE017259‐DE015437, and COLCIENCIAS (Bogotá, Colombia). Grant Funding Source: NIDCR DE017259 ‐ DE015437