Ludmila of Bohemia or Saint Ludmila (ca. 860–921) is a popular religious figure from the Czech Republic. In 2021, the reliquary containing part of her skull was scanned and the missing portion of the structure was digitally reconstructed using references from anthropological studies carried out in the late 1990s by Dr. Emanuel Vlček, Ph.D. (1925–2006). From the completed skull, an estimation of facial hard tissue made a forensic facial approximation possible. The present study aims to present the sequence of methodological analysis, the development of new techniques and procedures used in this case that can become tools to facilitate the task of digitally restoring skulls with missing structures that can be applied in archeological and surgical context. The cranial hard tissue from an anonymous donor of a CT-Scan exam was “deformed” to fit onto the remains of the historical skull of Ludmila of Bohemia. The estimated facial proportions were tested by several methods that correlate the proportions of cranial structures. The reconstruction was performed based on several scientific parameters and the resulting structures were also consistent to predictors commonly used in the forensic field. The cranial deformation method provided a hard tissue estimation and gave reference to a facial approximation of a historical figure. Its development and testing may inspire future research to support a wide range of applications that goes from archaeology to medical usage.