We use supported alumina templates and electrodeposition to fabricate self-standing Au-nanorods (Au-NR) arrays. Depending on electrolyte and deposition conditions two different NR morphologies with either corrugated or smooth topologies are fabricated. We show that the properties of the NR arrays, including amphiphilic and optical, very much depend on their morphology. Smooth NR arrays are hydrophobic while the corrugated ones are hydrophilic. Also the optical reflectance, though it shows plasmon resonances at very similar wave lengths, is much lower for the corrugated NR arrays. The activity of the NR arrays as substrates for molecular detection using Raman scattering, and Rhodamine 6G (R6G) as model dye, also strongly depends on their morphology. R6G concentrations down to 1 pM are detected on the corrugated arrays yielding an effective enhancement factor (EF) of approximately 1 × 10. In contrast an over-estimated (because of their hydrophobic character) EF of 6 × 10 is obtained for the smooth NR arrays.