3D printing technology is making its mark in automotive, aerospace, and bio-medical-related industries. It is considered a viable option for the direct manufacturing of final parts. However, it is not possible to print longer parts in a single attempt due to the bed size limitation of printers. This problem can be addressed by employing a polymer joining technique as a secondary operation. Moreover, low mechanical strength and inferior geometrical qualities like the flatness of the joined parts restrict its real-time industrial application. Here, an attempt is made to join a longer part (typical of an aircraft wing) using friction stir welding technique. Joining was performed on 3D printed similar/dissimilar thermoplastic parts. Tensile test results showed that friction stir welding of 3D printed parts (for both similar/dissimilar) produced relatively weaker joints compared to the base material. Various important process parameters of 3D printing and friction stir welding technique, namely part infill percentage, material combination, tool rotational speed, traverse speed, and tool pin taper angle were optimized by means of ANOVA. Optimization was aimed at maximizing the weld strength, elongation, hardness, and desired flatness. The results suggested that the material combination and tool pin taper angle play a significant role in the weld's strength as well as its geometric properties (flatness). The results were validated by adopting the optimized parameters for successful joining of the wing section of an unmanned aerial vehicle. A span of 320 mm, with a metrological acceptable flatness value of 0.41 µ/m could be successfully achieved on an existing 3D printer whose bed size limit was 240 mm.