In this work, we study surface enhanced Raman spectroscopy (SERS) active substrates with low background for the detection of Rhodamine 6G. In our experimental evaluations, the surface enhanced Raman scattering signals from the surface substrates with a duration of 12-hour treatment and without treatment are obtained. Through three-dimensional (3D) finite-difference time-domain (FDTD) numerical simulation, we find that the structures with vertical variations of surface have larger field enhancement than that of horizontal variations which implies a strong positive effect on the local field enhancement. Moreover, the field enhancements are sensitive to the diameter and the shape of Au nanoparticles. We further find the 35-nm cubic shape of Au nanoparticle shows relatively larger electric field enhancement than that of spherical one.