Octree DSMC is a domain independent methodology used to sort gas particles into nearest neighbors. For very irregular geometries immersed in the domain, the flexibility of the octree method is explored. Modifications made to the numerical approach to compute the volume of irregular octree clusters is presented. The accuracy of the modified octree DSMC is investigated by simulating standard test cases, such as the Fourier flow and micro-poiseuille flow. The octree DSMC simulation results match well with the traditional cartesian grid methods in both the test cases. To further expand its applicability to complex domains, two immersed geometries, a single spherical spore and a fractal-like spore aggregate structure, are first immersed in a 500 K heat bath. This is followed by placing the spores in a Mach 1.92 supersonic flow at 500 K temperature. A heat shielding effect is observed on the inner surface of the fractal spore structure from the heat flux computations. Results confirm that the octree DSMC method is both, accurate and flexible, to model heat transfer on highly irregular geometries embedded in the flow-field.