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This work investigates three-dimensional simulation of fused filament fabrication using the Cross-WLF model for the non-isothermal and shear thinning behavior of the melt. To realistically simulate the deposition flow, the acceleration, viscosity evolution, and flow front tracking models have been included with the pressure gradient in the deposited road and boundary modeling of the melt and air interface. The results indicate that the non-isothermal and shear thinning behaviors greatly affect the geometry of the deposited roads including the flow front and trailing cross-section shapes. The thermal footprint of the interface between the deposited melt and the substrate is also predicted as a function of the thermal contact conductance. The pressure distribution within the deposited road is also modeled and is found to be not symmetric with respect to the nozzle center-line. Rather, the pressure peak shifts slightly downstream due to redirection of the melt around a stagnation point opposite the nozzle exit. Furthermore, a negative stress is observed downstream the exterior nozzle face associated with the free expansion of the melt as the extruded material climbs and releases from the exterior nozzle face. The developed simulation is verified by comparison with experimental results providing contact pressures ranging from 5 to 132 kPa.