Gold and silver nanoparticles and nanostructures exhibit plasmon resonances that result in strong scattering and absorption of light, as well as enhanced optical fi elds near the metal surface. The resonant fi eld enhancement dramatically enhances the weak Raman scattering signals from molecules near the metal surface. [ 1 ] This effect, called surface enhanced Raman scattering (SERS), has been widely pursued as a molecular sensing technology over the past decade. [ 2 , 3 ] SERS is non-destructive, suffi ciently sensitive for single molecule detection, and provides inherent molecular specifi city since it yields molecular vibrational spectra. While fi eld enhancement occurs over an entire nanostructure surface, SERS signals are strongest from small gaps between nanoparticles referred to as "hot spots" where the fi eld enhancement is maximal. [ 4 , 5 ] Most SERS work to date has focused on detection with substrates that are designed to maximize the density, sensitivity, and reproducibility of hot spots in order to give the strongest possible SERS signal. Many substrates have been developed which refl ect the variety of nanofabrication, synthesis, and assembly strategies that have emerged over the past decade. These include semiconducting nanowires, [ 6 ] aggregated colloids, [ 7 , 8 ] colloidal lithography, [ 9 , 10 ] soft lithography, [ 11 , 12 ] e-beam lithography, [ 13 ] and colloidal assembly. [ 14 , 15 ] Most of the substrates consist of nanostructured gold or silver on a fl at substrate. Some reports describe substrates with increased surface roughness to increase the number of hot spots, including aligned carbon nanotube substrates that support silver nanoparticles. [ 16 ] These substrates were found to provide highly sensitive detection. However, optical scattering and light collection occur in a three dimensional focal volume. Therefore, to maximize the quantity of scattered light generated and detected, SERS substrates should contain hot spots in a large three dimensional volume that is matched to the optics of the SERS instrumentation. Three dimensional substrates have been fabricated and tested based on porous silicon, microfabricated silicon, and porous gold. [17][18][19][20] These have indeed improved the detection limit for small molecules like trinitrotoluene (TNT). Therefore, it is desirable to create densely packed metal nanostructures with nanogaps to form plentiful hot spots for better SERS performance. [21][22][23] In the present study, we describe the fabrication of a structurally tunable 3D SERS substrate based on vertically aligned CNTs. Vertically aligned CNTs provide a new paradigm to realize three dimensional SERS substrates with high nanoparticle density. The vertically aligned CNTs were synthesized on a SiO 2 substrate by water-assisted chemical vapor deposition (CVD). The resulting vertically aligned CNTs were several millimeters long and were composed of a mixture of double-and triple-walled nanotubes. [ 24 , 25 ] A gold fi lm (50 nm thickness) was deposited on top of the CN...