In this paper we theoretically consider the physical mechanisms behind the surface-enhanced Raman scattering (SERS) enhancement produced by commercially available Klarite substrates, which consist of rectangular arrays of micrometre-sized pyramidal pits in silicon with a thin gold coating. Full three-dimensional numerical simulations of the pits are conducted for both a real gold metal coating and a perfect electrical conductor (PEC) to determine whether the SERS enhancement is due to diffraction or plasmon effects. The pit apex angle and metal coating thickness are also varied to determine whether it is possible to further enhance the SERS signal by optimising the structural parameters of these substrates. By decreasing the film thickness and adjusting the apex angle, it is possible to achieve an enhancement almost double that of a standard Klarite substrate. Copyright © 2010 John Wiley & Sons, Ltd.