One of the major drawbacks of the thermoplastic Fused Filament Fabrication process (FFF) is the poor mechanical properties of the parts produced. This is mostly related to the macroporosities resulting from a limited coalescence between filaments. Coalescence is ruled by the viscosity and surface tension of a polymer. Thus, an accurate characterization of these two properties is required to model and optimize coalescence during filament deposition and cooling. In this work, a surface tension characterization procedure over a large temperature range (25–380 °C) is presented and applied to PolyEtherKetoneKetone (PEKK) material. Additionally, the Newtonian viscosity is characterized with rheometry. The coalescence is then simulated by coupling an existing semi-analytical model with a previously presented 2D heat transfer finite element simulation model. The results show the importance of the temperature dependent implementation of surface tension. Additionally, a parametric study provides an industrial understanding of the FFF process.