We studied the growth mode of vertically aligned carbon nanofibers (CNFs) on Ni catalyst strips fabricated using a focused ion beam (FIB). We found that the CNF growth on Ni catalysts was strongly affected by the geometry of the microfabricated Ni catalyst strips. Selective growth of vertically aligned CNFs requires ion milling from the outside edge of the sample so that the milled materials are effectively evacuated. The CNF diameter and density on the strip depends on its width. Possible mechanisms to control CNF growth using microfabricated catalysts are analyzed with a liquid model using surface free energies.