One of the current efforts in aerospace industry is to reduce weight of the structures by developing new lightweight high-performance materials. High temperature resistant thermoplastics such as polyetheretherketone (PEEK) and polyetherimide (PEI) are excellent choices due to their high mechanical properties close to the aerospace materials specifications. With the increasing interest in additive manufacturing (AM), or 3D printing, of complex shape structures in the aerospace industry, the AM of PEEK and its fiber-reinforced composites are foreshadowed to be highly demanding. The main objective of this study is to design processable and printable carbon fibers (CFs) reinforced PEEK composite filaments for Fused Filament Fabrication (FFF). The special focus is on the microscopic structure of the material and the mechanical properties of 3D printed filaments. First, PEEK and CFs are mixed in a twin-screw micro-compounder (Xplore) to obtain composite filament with a diameter close to 1.5mm. The filament is then fed into a commercial FFF 3D printer (AON3D) to fabricate a filament with uniform, smaller diameter of around 0.6mm. The resulting filament was observed under Scanning Electron Microscopy (SEM) showing that CFs are well dispersed in and well adhered to the PEEK matrix. This observation is in good agreement with the results obtained from the tensile test on 3D printed filaments which showed good mechanical properties obtained by the addition of CFs to the matrix. Finally, we use a Micro-CT to get an optimal view of the core structure of the filament which provide additional information such as CFs length after processing, porosity/void content, etc. The result confirm that our developed materials are printable and can reach high mechanical properties suitable for aerospace applications. Keywords: FFF; 3D printing, Additive manufacturing; Micro-CT; SEM; Characterization