Atmospheric pressure plasma jet (APPJ) based modification as a facile method to modify the intimal surface of small caliber nanofibrous tubular tissue scaffolds for potential use as vascular-graft or spinal-cord conduit is reported here. Polycaprolactone, a biomaterial used in the US Food and Drug Administration approved scaffolds for various tissue regeneration and bioabsorbable suture applications, was electrospun into thin nano/microfibers to form seamless three-dimensional (3D) conduits of 4 mm intimal diameter. The 3D conduits were subjected to treatment with an APPJ produced by dielectric barrier discharge using controlled gas flow into ambient atmosphere. He/air or He/air/NH3 gas mixtures combined with 8.5 kV pulsed direct current signal proved effective in creating a sustained and reactive cold plasma jet to modify the intimal surface of tubular scaffolds without affecting its biomechanical properties. The treatment resulted in surface chemistry modification as indicated by enrichment of oxygenated functional groups. Surface chemistry was determined via x-ray photoelectron spectroscopy. Scanning electron microscopy and glycerol contact angle measurements were used to determine the surface morphology and surface wettability. The data support the conclusion that APPJ is as an effective, facile, and robust approach to modify the intimal surface of small-caliber (<4 mm) tubular conduits (successfully accomplished and initially reported here) for potential applications in vascular and neural tissue engineering.