Nanostructure characterization of carbon nanofibers (CNFs) for on-chip interconnect applications is presented. We propose a novel technique for characterizing interfacial nanostructures of vertically aligned CNFs, optimally suited for cross-sectional imaging with scanning transmission electron microscopy (STEM). Using this technique, vertically aligned CNFs are selectively grown by plasma-enhanced chemical vapor deposition (PECVD), on a substrate comprising a narrow strip (width ~100nm) formed by focused ion beam (FIB). Using high-resolution STEM, we show that CNFs with diameters ranging from 10-100 nm exhibit very similar graphitic layer morphologies at the base contact interface