The phenomenon of extraordinary optical transmission (EOT) due to its advantages has been considered by researchers in various applications and in recent years many efforts have been made to engineer these structures to get the best possible response for desired applications. In this work, the optical properties of novel binary gold nano-hole arrays are investigated theoretically. We engineered the optical response of the system by adjusting the ratio of contribution of surface plasmon polariton (SPP) to localized surface plasmon resonance (LSPR) through the manipulation of the geometrical properties. The changes in the topology of this nano-hole array affected the intensity and the wavelength of transmission peaks. The sensitivity of the optical response to the refractive index was also investigated. The designed structure is a good candidate for use as a polarization-independent optical label-free sensor.