This paper analyzes the effect of Fourier vs. subcontinuum heat transport through thin layers of nanoporous silica (aerogel) in the framework of an infrared focal plane array (IRFPA) sensor system. Aerogel is introduced as a compatible material for emerging microsystems applications and the comparison between aerogel and conventional insulation systems is analyzed. Correlations between aerogel’s macro-scale thermal properties and its nano-scale structure are discussed to address the effect of the material’s amorphous structure and sub-continuum phonon transport phenomena on macro-scale thermal conductivity. Simulations using the Lattice Boltzmann Method (LBM) quantify the effect of phonon scattering on silica conductivity. Techniques for extending the analysis to a three-dimensional silica matrix are discussed in light of recent advances in the simulation of aerogel morphology.