In this work, the two-photon-polymerization (TPP) fabrication technique was employed for the first time to manufacture with success three-dimensional (3D) micro-structures suitable for confined rarefied gas flows. Four different micro-tubes of simple geometry have been tested in vacuum conditions. The geometry of the micro-tubes was characterized via a focus-variation 3D optical measurement microscope, a digital microscope and a X-ray µ-tomography. Mass flow rate measurements of pressure-driven rarefied gas flows of nitrogen in slip and transition regimes are were compared to theoretical values obtained via the kinetic theory of gases. The experimental measurements were realized via the constant volume technique. The good agreement obtained between experimental and numerical results proves the feasibility of using this fabrication technique to create well controlled 3D shaped microsystems for rarefied gas flows applications.