Fused Filament Fabrication (FFF) is an Additive Manufacturing (AM) technique where a filament of molten polymer is extruded from a die onto a substrate to build a three dimensional object layer-by-layer. AM is the opposite of Subtractive Manufacture (SM) where material is removed from a precursor through machining or other means. The FFF process uses counter-rotating gears to push a ca. 1-3 mm diameter fiber into a heated die, in which it is melted or softened, and acts like a continuous piston constantly pushing the melt forward. The molten polymer is extruded through a small capillary die (nozzle) onto already deposited material and by moving the extruder and/or substrate a part is fabricated layer-by-layer. Heat transfer and rheology are very important in the FFF process. We find heat transfer is limiting in FFF due to the nature of the flow and the potential for fouling. This was determined by monitoring the temperature and pressure in the FFF instrument and comparing the results to classic heat transfer models. Thus, to improve the FFF processing rate better heat transfer is required. In addition, the ultimate strength of any fabricated object is dictated by how well the tracks weld together. We developed a heat transfer model and it accurately predicts the temperature at the weld line. We determined the reptation time as a function of temperature to find how well the interface has healed since molecules must diffuse across the original interface for object strength to develop. This combined with the heat transfer model allows prediction of interfacial strength. The degree of healing, defined as the interface strength relative to the bulk strength, was calculated and compared to experimentally measured values to find surprisingly accurate predictions. From this, the process can be optimized. So, by increasing the heat transfer in the process and optimizing processing parameters it is expected to develop much stronger 3D printed parts.