Interest in digital twins has grown rapidly in recent years, both in science and industry. Moreover, due to their inherent ability to preserve fragile information, i.e., exposed to the risk of loss, digital twins have become relatively common in archeology. However, far from being just digital copies that allow one to learn about, share, preserve or even just enjoy an artifact without the need to be at the location of the original physical entity, a digital twin is a dataset that can evolve dynamically as new information becomes available or as the reference object changes. With this idea in mind, the present work focuses on a multidisciplinary research activity devoted to modeling the early medieval church of Santa Sofia in Benevento, Italy, which has undergone alterations in its geometric and structural layout several times throughout its long history. To track these modifications, starting with a laser scanner survey of the church in its current state, a model was constructed that includes five main archaeological and architectural phases backwards in time. The process, which made use of both open source and proprietary software, presented different levels of difficulty, with some parts very easy to draw and others requiring specific geometric analysis. In particular, to upload the complex vault system of the church into the model, a homemade computer code was written, aimed at reconstructing surfaces from the point cloud making use of Coons patches based on Hermitian cubics.