Terrestrial laser scanning is a widely used technology to digitise archaeological, architectural and cultural heritage. This allows for modelling the assets’ real condition in comparison with traditional data acquisition methods. This paper, based on the case study of the basilica in the Baelo Claudia archaeological ensemble (Tarifa, Spain), justifies the need of accurate heritage modelling against excessively simplified approaches in order to support structural safety analysis. To do this, after validating the 3D meshing process from point cloud data, the semi-automatic digital reconstitution of the basilica columns is performed. Next, a geometric analysis is conducted to calculate the structural alterations of the columns. In order to determine the structural performance, focusing both on the accuracy and suitability of the geometric models, static and modal analyses are carried out by means of the finite element method (FEM) on three different models for the most unfavourable column in terms of structural damage: (1) as-built (2) simplified and (3) ideal model without deformations. Finally, the outcomes show that the as-built modelling enhances the conservation status analysis of the 3D heritage city (in terms of realistic compliance factor values), although further automation still needs to be implemented in the modelling process.