We have successfully prepared SERS-active substrates for the detection of both Rhodamine 6G. The electric field enhancement could be controlled by tuning the surface roughness of the substrates through varying treatment duration. Through the 3D FDTD simulation, the results have shown that the field enhancement of spherical nanopatcles with 100% height variation is sizeable. It has implied that the roughened surface could get larger enhancement. The different shape of nanopartcles also can be fabricated by other synthesis method for local field enhancement in diverse nano-biosensor application and is currently under consideration.