Cellular adhesion and proliferation inside three-dimensional synthetic scaffolds represent a major challenge in tissue engineering. Besides the surface chemistry of the polymers, it is well recognized that scaffold internal architecture, namely pore size/shape and interconnectivity, has a strong effect on the biological response of cells. This study reports for the first time how polycaprolactone (PCL) scaffolds with controlled micro-architecture can be effectively produced via bioextrusion and used to enhance the penetration of plasma deposited species. Low-pressure nitrogen-based coatings were employed to augment cell adhesion and proliferation without altering the mechanical properties of the structures. X-ray photoelectron spectroscopy carried out on different sections of the scaffolds indicates a uniform distribution of nitrogen-containing groups throughout the entire porous structure. In vitro biological assays confirm that plasma deposition sensitively promotes the activity of Saos-2 osteoblast cells, leading to a homogeneous colonization of the PCL scaffolds.