Plasmonic nano-structures are important for many photonic devices and applications. The optical transmission spectra of such structures are extraordinary. In this paper, we investigate the optical transmission spectra of thin gold films perforated with imperfect circular nano-hole arrays using the finite difference time domain (FDTD). It is observed that both of the intensity and resonance positions of the transmission spectra of perfect plasmonic circular nano-hole arrays are strongly modified due to nano-holes imperfection. Furthermore, we comprehensively study the transmission spectrum of plasmonic spherical nano-hole arrays as a simple example for hole imperfection.