Understanding of near-field radiative transfer is crucial for many advanced applications such as nanoscale energy harvesting, nano-manufacturing, thermal imaging, and radiative cooling. Near-field radiative transfer has been shown to be dependent on the material and morphological characteristics of systems, the gap distances between structures, and their temperatures. Surface interactions of phononic materials in close proximity of each other has led to promising results for novel near-field radiative transfer applications. For systems involving thin films and small structures, as the dimension(s) through which the heat transfer takes place is/are on the order of sub-micrometers, it is important to identify the impacts of size-related parameters on the results. In this work, we investigated the impact of geometric design and characteristics in a double-layer metamaterial system made up of GaN, SiC, h-BN, all of which have potential importance in micro-and nano-technological systems. The numerical study is performed using the NF-RT-FDTD algorithm, which is a versatile method to study near-field thermal radiation performances of advanced configurations of materials, even with arbitrary shapes. We have systematically investigated the thin film thickness, the substrate material, and the nanostructured surfaces effects, and reported on the best combination of scenarios among the studied cases to obtain maximum enhancement of radiative heat transfer rate. The findings of this work may be used in design and fabrication of new corrugated surfaces for energy harvesting purposes. (C) 2018 Elsevier Ltd. All rights reserved.