We have fabricated diamond-like silicon photonic crystals through a sequential silica/silicon chemical vapor deposition (CVD) process from the corresponding polymer templates photopatterned by holographic lithography. Core-shell morphology is revealed due to the partial backfilling of the interstitial pores. To model the shell formation and investigate its effect to the bandgap properties, we developed a two-parameter level-set approach that closely approximated the core-shell morphology, and compare the bandgap simulation with the measured optical properties of the 3D crystals at each processing step. Both experimental and calculation results suggest that a complete filling is necessary to maximize the photonic bandgap in the diamond-like structures.