This study presents a methodology for developing and validating digital models of tooth-inlay systems, aiming to trace the complete workflow from clinical procedures to simulation by involving dental professionals—dentists for manual cavity preparation and dental technicians for restoration modelling—while integrating micro-computed tomography (micro-CT) imaging with finite element analysis (FEA). The proposed workflow includes (1) the acquisition of high-resolution 3D micro-CT scans of a non-restored tooth, (2) image segmentation and reconstruction to create anatomically accurate digital twins and mesh generation, (3) the selection of proper resin and the 3D printing of four typodonts, (4) the manual preparation of cavities on the typodonts, (5) the acquisition of high-resolution 3D micro-CT scans of the typodonts, (6) mesh generation, digital inlay and onlay modelling and material property assignment, and (7) nonlinear FEA simulations under representative masticatory loading. The approach enables the visualisation of stress and deformation patterns, with preliminary results indicating stress concentrations at the tooth-restoration interface integrating different cavity alternatives and restorations on the same tooth. Quantitative outputs include von Mises stress, strain energy density, and displacement distribution. This study demonstrates the feasibility of using image-based, tooth-specific digital twins for biomechanical modelling in dentistry. The developed framework lays the groundwork for future investigations into the optimisation of restoration design and material selection in clinical applications.