Fused filament fabrication (FFF) is a type of additive manufacturing based on material extrusion that has long been considered a prototyping technology. However, the right application of material, process, and product can be used for manufacturing of end-use products, such as air-cooled heat exchangers made by adding fillers to the base polymer, enhancing the thermal conductivity. Fiber fillers lead to anisotropic thermal conductivity, which is governed by the process-induced fiber orientation. This article presents an experimental study on the microstructure-property relationship for carbon fiber-filled polyamide used in FFF. The fiber orientation is measured by micro-computed tomography, and the thermal conductivity of manufactured samples is measured. Although the thermal conductivity is raised by more than three times in the fiber orientation direction at a load of only 12 vol.%, the enhancement is low in the other directions, and this anisotropy, along with certain manufacturing restrictions, influences the final part performance.