This paper introduces an enhanced method to generate 3D prints of individual joining gaps in the automated assembly. Therefore the automated processes of surface measurement, virtual construction and additive manufacturing are combined to realize an Industry 4.0 compatible 'Smart Factory'. The gap between two parts is calculated prior to physical assembly by measuring the joining surfaces optically. The two joining parts are assembled virtually with an automated gap analysis. Therefore the surface measurements are virtually aligned. To fill the gap with solid material, the gap is 3D printed with a new method processing two geometrically non combined point clouds to one closed volume model that represents the joining gap. Areas with gaps smaller than an assembly specific threshold are automatically omitted during printing. A methodology to reduce surface errors is performed and the 3D gap model is exported in a standardized file format to a printer. This process ensures a fully automated assembly and therefore a faster production. The described method is evaluated and tested on a one-to-one scale assembly cell for next generation vertical tail planes.