A challenge for tissue engineering is to produce synthetic scaffolds of adequate chemical, physical and biological cues effectively. This paper describes a plasma-assisted bio-extrusion system to produce functional-gradient scaffolds; it comprises pressure-assisted and screw-assisted extruders, and plasma jets. This paper also describes how the system conducts plasma surface modification during the polycaprolactone scaffold fabrication process. Water contact angle and in vitro biological tests confirm that the plasma modification alters the hydrophilicity properties of synthetic polymers and promotes proliferation of cells, leading to homogeneous cell colonization. The results suggest this system is promising for producing functional gradient scaffolds of biomaterials.