The observation and the interpretation of line splitting in photoluminescence and cathodoluminescence spectra of GaAs/AlGaAs V-groove quantum wires (QWRs) are reported. The QWR emission line splits into two peaks whose intensities oscillate systematically along the axis of the wire. Combining atomic force microscopy and cathodoluminescence measurements, we show a clear correlation between the surface topography of the V-groove and the individual peak intensities. We elucidate the relationship between the V-groove sidewall roughness and the shape at its bottom, and explain their impact on the QWR formation using a two-dimensional growth model accounting for self-limited growth in each V-groove domain. The influence of the long-range substrate roughness on the QWR spectral features is thus clarified. The study provides guidelines for improving QWR uniformity in order to achieve near-ideal model systems for one-dimensional semiconductors