This work presents Computational Fluid Dynamics (CFD) simulations of the polymer flow inside the hot-end during material extrusion additive manufacturing. Two CFD models are investigated: a previously-published one-phase model, where the entire domain is filled with liquid, and a novel model, where the free surface of the polymer inside the channel is resolved. Both models predict a recirculation region between the nozzle wall and the incoming filament. With the free surface resolved, melting of the solid filament and filling of an empty liquefier channel are shown in detail. Moreover, the simulations predict the pressure and temperature distributions inside the channel. The molten polymer (ABS) is simulated as a Generalized Newtonian Fluid with shear- and temperature-dependent viscosity. The numerical results are compared with the experimental measurements of the filament feeding force, which relates to the pressure inside the flow channel. An inverse analysis of the heat transfer coefficient is performed to estimate the thermal resistance at the channel’s wall. It is shown that the model which resolves the free surface is able to predict the feeding force for typical working conditions with a reasonable accuracy. Moreover, it captures the change of the flow regime from stable to unstable extrusion at high feeding rates. A hypothesis that explains the pressure and melt zone oscillations that occur during unstable extrusion is given. The influence of the liquefier temperature, liquefier length and nozzle diameter on the flow are discussed. The predictions of the model become less accurate when different channel geometries are simulated, which is attributed to the simplified material model that does not capture viscoelastic effects and possible buckling of the solid filament.