Atomistic models of two different fluorinated polybenzoxazoles, 6F-PBO and 3F-PBO, were used to simulate the amorphous structures of these polymers. Molecular mechanics and molecular dynamics techniques were utilized to relax the independent structures from an initial high-energy system. The relaxed model structures showed 6F-PBOs to be more coiled relative to 3F-PBO. Conformational grid search was performed on each of the repeat units to analyze the local structure of the two polymeric backbones. The torsional angles corresponding to energy minima and rotational barrier were found to vary between the 6F and 3F structure due to differences in the pendant group at the C-alpha carbon atom. The Hildebrand solubility parameters and elastic constants for the two different polymers were estimated from simulation. 3F-PBO is predicted to possess a higher solubility parameter and higher moduli compared to the GF-PBO.