Additive manufacturing (AM) is a production method that enables the building of porous structures with a controlled geometry. However, there is a limited control over the final surface of the product. Hence, complementary surface engineering strategies are needed. In this work, design of experiments (DoE) was used to customize post AM surface treatment for 3D selective laser melted Ti6Al4V open porous structures for bone tissue engineering. A two-level three-factor full factorial design was employed to assess the individual and interactive effects of the surface treatment duration and the concentration of the chemical etching solution on the final surface roughness and beam thickness of the treated porous structures. It was observed that the concentration of the surface treatment solution was the most important factor influencing roughness reduction. The designed beam thickness decreased the effectiveness of the surface treatment. In this case study, the optimized processing conditions for AM production and the post-AM surface treatment were defined based on the DoE output and were validated experimentally. This allowed the production of customized 3D porous structures with controlled surface roughness and overall morphological properties, which can assist in more controlled evaluation of the effect of surface roughness on various functional properties.