The flow of fluid in seal applications is known to be elastohydrodynamic, with the gap being extremely narrow. Additive manufacturing is known to produce minimal differences in surface structure compared to the required surface. However, the presence of even slight variations in surface structures can have a significant impact on the gap flow. This research aims to explore the changes in flow and resulting forces due to the use of 3D printed surface structures on dynamic rod seals. The study utilizes numerical simulations conducted using the finite element method (FEM) and the program code COMSOL. Fully coupled fluid-structure interaction (FSI) simulations were used to compare the behavior of seals with smooth, structureless edges to those with edges featuring structured 3D printed surfaces according to the individual layers in a fused-deposition-modeling (FDM) printing process. Three different models were developed, each representing a different level of printing quality and surface roughness: the ”ideally smooth” model, the ”coarse AM” model, and the ”fine AM” model. One of the challenges of this study was that different solutions changed their numerical stability properties with increasing sliding velocity. Stable solutions became unstable, and vice versa. The influence of the different surfaces on axial and radial fluid forces was evaluated, and the coefficients of friction were determined to make predictions about tribological properties. With a fully meshed fluid volume, it was possible to evaluate velocities and pressures in the fluid. The research found that the 3D printed surface significantly changed the gap flow, resulting in a change in the coefficient of friction. Eddy generation was observed on the 3D printed surface, and there was a stepwise loss of contact from sliding friction to fluid friction. Overall, the study demonstrated that even slight variations in surface structure resulting from 3D printing can have a significant impact on the flow of fluid in seal applications, ultimately affecting the resulting forces and tribological properties.