The member stiffness and pressure distribution in a bolted joint is significantly influenced by the contact area of the mechanical interface under a prescribed preload force. This research explores the influence of as-built surface profiles for nominally flat interfaces of a C-Beam assembly with two well-defined contact regions. A high-fidelity finite element model is created such that the model uncertainty is minimized by updating and calibrating the piece parts prior to the preload assembly procedure. The model is then assembled and preloaded to evaluate the contact stresses and contact area for both nominally flat and perturbed non-flat surfaces based on three-dimensional surface topography measurements. The predicted pressures are validated with digitized pressure-sensitive film measurements. The high-fidelity modeling reveals how the compliance and thickness of the pressure-sensitive film alter the measured pressures, leading to incorrect evaluations of the stresses and contact area in the joint. The resulting low-level dynamic behavior of the preloaded assembly is shown to be sensitive to the true contact area by linearizing the nonlinear finite element model about the preloaded equilibrium and performing a computational modal analysis. The resonant frequencies are validated with experimental measurements to demonstrate the effect of the contact area on the modal characteristics of the bolted assembly. Vibration modes and loading patterns exhibit varying levels of sensitivity to the contact area in the joint, leading to an improved physical understanding of the influence of contact mechanics on the low-level linear vibration modes of jointed assemblies.