In this work, we computationally study surface enhanced Raman spectroscopy (SERS) active substrates and their application in the detection of Rhodamine 6G (R6G). To examine the electromagnetic enhancement, we first apply the finite-difference time domain (FDTD) algorithm to analyze the SERS active substrates by solving a set of Maxwell's equations (Ampere's Law and Faraday's Law) in differential form. The local field enhancements are simulated in the visible regime with the wavelength of 633 nm. Through the three-dimensional (3D) FDTD simulation, we find that the roughened surface have relatively larger field enhancement following the Beckmann-Kirchhoff theory and can be achieved by hydrothermal treatment. Also the enhancements with different shape of nanoparticle are tested and obtained which are nanoparticle, gold nanocage and gold/silver alloy for spherical, cubic and pyramidical shapes. The results show that the enhancement of spherical and cubic shapes can be much improved by nanocage and gold/siliver alloy structures.