In this work, we investigate the impact of nano-scale pores within structured metamaterials on spectral near-field radiative transfer. We use Finite Difference Time Domain Method (FDTD) and consider uniform and corrugated SiC substrates filled with rectangular nano-scale vacuum inclusions having equivalent diameters of 10, 37 and 57 nm. We report the appearance of the secondary and tertiary resonance peaks at different frequencies as a function of changing pore diameter, which cannot be predicted if an effective medium theory approximation is used.