We report the large-area alignment of multi-segmented nanowires in nanoscale trenches facilitated by capillary forces. Electrochemically synthesized nanowires between 120 and 250 nm in length are aligned and then etched selectively to remove one segment, resulting in arrays of nanowires with precisely controlled gaps varying between 2 and 30 nm. Crucial to this alignment process is the dispersibility of the nanowires in solution which is achieved by chemically modifying them with hexadecyltrimethylammonium bromide. We found that, even without the formation of an ordered crystalline phase at the droplet edges, the nanowires can be aligned in high yield. To illustrate the versatility of this approach as a nanofabrication technique, the aligned nanowires were used for the fabrication of arrays of gapped graphene nanoribbons and SERS substrates.