Precise arrangement of nanoscale elements within larger systems, is essential to controlling higher order functionality and tailoring nanophase material properties. Here, we present findings on growth conditions for vertically aligned carbon nanofibers that enable synthesis of high density arrays and individual rows of nanofibers, which could be used to form barriers for restricting molecular transport, that have regular spacings and few defects. Growth through plasma-enhanced chemical vapor deposition was initiated from precisely formed nickel catalyst dots of varying diameter and spacing that were patterned through electron beam lithography. Nanofiber growth conditions, including power, precursor gas ratio, growth temperature and pressure were varied to optimize fiber uniformity and minimize defects that result from formation and migration of catalyst particles prior to growth. It was determined that both catalyst dot diameter and initial plasma power have a considerable influence on the number and severity of defects, while growth temperature, gas ratio (C(2)H(2):NH(3)) and pressure can be varied within a considerable range to fine-tune nanofiber morphology.