When designing joined structures, deterministic approaches are commonly considered insufficient to ensure a good compromise between mechanical performances and manufacturing tolerances due to the many sources of variability. Reliability-based design approaches are promising, but they require structural models that take into account the different sources of variability and the complex physical phenomena that govern their effects on mechanical behaviour. This paper proposes a method to analyse the fastening process of parts that include geometric form defects. The structural behaviour of the joint is simulated using a finite element model combining connectors and rigid surfaces to represent fasteners. With this approach, the calculation time can be drastically reduced while frictional contact is maintained between fasteners and parts. Shape defects are generated by translating parts mesh nodes. The method is applied to a case study and its efficiency is evaluated by analysing the evolution of axial bolt preloads and transverse bolt forces during the assembly process. Results demonstrate the ability of the method to simulate different clamping sequences and to capture the interaction between shape defects, bolt-hole clearance and target axial preload.