Recent advances in Fused Filament Fabrication (FFF) include large material deposition rates and the addition of chopped carbon fibers to the filament feedstock. During processing, the flow field within the polymer melt orients the fiber suspension, which is important to quantify as the underlying fiber orientation influences the mechanical and thermal properties. This paper investigates the correlation between processing conditions and the resulting locally varying thermal-structural properties that dictate both the final part performance and part dimensionality. The flow domain includes both the confined and unconfined flow indicative of the extruder nozzle within the FFF deposition process. The resulting orientation is obtained through two different isotropic rotary diffusion models, the model by Folgar and Tucker and that of Wang et al., and a comparison is made to demonstrate the sensitivity of the deposited bead's spatially varying orientation as well as the final processed part's thermal-structural performance. The results indicate the sensitivity of the final part behavior is quite sensitive to the choice of the slowness parameter in the Wang et al. model. Results also show the need, albeit less than that of the choice of fiber interaction model, to include the extrudate swell and deposition within the flow domain.