A key factor to the implementation of devices with vertically aligned carbon nanofibers (VACNFs) is fundamental understanding of how to control fluctuations in the growth direction of the fibers. Here we demonstrate synthesis of VACNF on transparent and insulating substrates by continuous direct current (DC) plasma for realization of cellular interface suitable for transmission optical microscopy. To maintain continuous glow discharge above the substrate, a metal grid electrode layer (Cr) was deposited over silica with windows of exposed silica ranging in size from 200 μm to 1 mm. This electrode geometry allows for synthesis of VACNFs even within an insulating window. This observation and the observed trends in the alignment of nanofibers in the vicinity of grid electrodes have indicated that the alignment does not correspond to the direction of the electric field at the substrate level, contrary to previously proposed alignment mechanism. Computational modeling of the plasma with this grid cathode geometry has shown that nanofiber alignment trends follow calculated ion flux direction rather than electrical field. The new proposed alignment mechanism is that ion sputtering of the carbon film on a catalyst particle defines the growth direction of the nanofibers. With this development, fiber growth direction can be better manipulated through changes in ionic flux direction, opening the possibility for growth of nanofibers on substrates with unique geometries.