The optical performance of nanostructured gradient index vortex phase masks (VPMs) in various external media was investigated. We utilized a modified stack-and-draw technique to fabricate the microscopic-size masks. Its structure contains spatially distributed sub-wavelength rods made of two thermally matched glasses with high and low refractive indices. Measured optical characteristics of the generated vortices with azimuthal phase distribution are presented. The numerical and experimental study shows that such VPMs with the same designed structure but varied thickness can convert fundamental light beam into optical vortices with different charges. Furthermore, we found that the mask performance is unaffected by the refractive index of the surrounding media making it an excellent candidate for microfluidic applications.