One of the major drawbacks in thermoplastic Fused Filament Process (FFF) is the poor mechanical properties of the parts compared to bulk parts obtained by thermoplastic injection, especially in the transverse direction. This is related to (i) the porosities between deposited filaments and (ii) the limited adhesion between deposited layers. The porosities evolution is thermally driven through coalescence between filaments. The evolution of interface between filaments is ruled by viscosity and surface tension. A precise characterization of these two thermal dependent properties is then required to model accurately the heat transfer at the scale of the filament. We propose in this work to detail the characterization procedure as well as the results obtained for PAEK material with temperature up to 400°C. The evolution of the coalescence is then obtained by coupling a modified Frenkel’s model with heat transfer in a 2D finite element model. Results are finally compared with the shape of real printed filaments in a home-made 3D printer for high-temperature polymers.