The Fused Filament Fabrication process is the most widely used process for prototyping. The use of variable feedstock material, specimen geometries, pre-processing software, and printers makes comparability and reproducibility challenging, because the part properties not only change with varying print parameters, but also with changes in the slicing routine and tool path generation. The sequential part build-up causes a transient temperature field that affects the local microstructure and interfacial bonding and thus the macroscopic properties. The weld line formation between neighboring beads within layers as well as between layers has been identified as one of the biggest factors affecting mechanical properties. To circumvent these constraints and study the temperature field, a custom python™ program was developed and programed, which allows control over traditional user adjustable print parameters, such as print speed, but also infill angle, custom infill patterns, distance between beads, and amount of material extruded along a bead. Using this tool path generation tool the cooling and re-heating effect during printing was studied using an IR thermal camera and additional thermocouples on the build platform. Varying the nozzle temperature, print speed, layer height and material properties, it was shown that all paremeters have all significant effect on the cooling of the newly deposited layer and the re-heating of previously deposited layers. The re-heating of the layers above the glass transition temperature can be correlated to the resulting weld strength in the printed specimens. A numerical analysis in ANSYS Mechanical using the element death and birth effect proved that radiation should be included because of the initially high deposition temperatures, and that the presence and size of voids affect the re-heating or cooling rate during the deposition process.