In this work, a linear space filling Morton Z-curve is employed to represent the three dimensional octree structure in an array. The advantages and implementation of this linearized octree for the Direct Simulation Monte Carlo (DSMC) method is demonstrated. A hybrid MPI-CUDA multi-GPU solver is used to model gas flow through two types of immersed bodies, a fractal-like spherical aggregate and a fibrous microstructure of a Morgan carbon Felt material. The permeability of this material is calculated by modeling the diffusion of argon gas and the calculated continuum permeability values match very well with other published data. Strong scaling has shown that the multi-GPU octree-based DSMC solve is 85% efficient with 16 GPUs for a large-scale problem.