Pre-processing of CAD models derived from Digital Mock-Ups (DMUs) into finite element (FE) models is usually completed after many tedious tasks of model preparation and shape transformations. It is highly valuable for simulation engineers to automate time-consuming sequences of assembly preparation processes. Here, it is proposed to use an enriched DMU with geometric interfaces between components (contacts and interferences) and functional properties. Then, the key concept of template-based transformation can connect to assembly functions to locate consistent sets of components in the DMU. Subsequently, sets of shape transformations feed the template content to adapt components to FE requirements. To precisely monitor the friction areas and the mesh around bolts, the template creates sub-domains into their tightened components and preserves the consistency of geometric interfaces for the mesh generation purposes. From a user-selected assembly function, the method is able to robustly identify, locate and transform groups of components while preserving the consistency of the assembly needed for FE models. To enlarge the scope of the template in the assembly function taxonomy, it is shown how the concept of dependent function enforces the geometric and functional consistency of the transformed assembly. To demonstrate the proposed approach, a business oriented prototype processes bolted junctions of aeronautical structures.