In recent years, there has been an increasing attention towards the use of the BIM (Building Information Modeling) approach in the cultural heritage domain. The stringent regulatory requirements in terms of BIM adoption in the field of public works in the short term will also have an impact on the historical heritage that characterises most European cities. However, when it comes to historical architecture, especially if it is in a state of ruin/abandonment, several critical issues arise. The first issue concerns the geometric simplification of architectural components provided by common commercial BIM platforms, that leads to search for other solutions. Another theme is the software interoperability, when sharing data between different platforms in order to enrich the digital model with not geometric information. Therefore, this research explores the concept of model tolerance and level of accuracy referring to a very complex architectural building. As case of study the church of Santa Maria delle Grazie in ancient Misterbianco (Sicily) has been chosen. The church was covered by the Etna eruption of 1669 and was recently brought to light during the excavations carried out by the Superintendence to Cultural Heritage of Catania. The state of decay of the church (warped floor, curved and out of lead walls, deteriorated altars and undamaged surfaces) makes it an excellent test bench on which to explore all the emerged criticalities, set up a feasible workflow and define a Level of Accuracy for complex or ruined architectural heritage.