Controlling the micro and nanostructure of materials is highly beneficial in order to tailor\ua0their physical properties. Extrusion-based 3D printing is a promising tool to produce\ua0hierarchical structures with controlled architecture. Combining additive manufacturing and\ua0self-assembled materials, complex structures with high anisotropy can be created. Lyotropic\ua0liquid crystals offer a wide variety of structures and compositions, in which hexagonal andlamellar phases are very interesting options. Far from the idealistic concepts of 3D printing\ua0and extrusion, the variability of the different systems, physical properties of the inks and\ua0environmental conditions play a fundamental role in the appearance of imperfections,\ua0undesired nanostructures and the limitation in the maximum effective alignment achieved.\ua0To understand the mechanisms that induce alignment in liquid crystalline phases and produce\ua0secondary effects and imperfections, a combination of different methods was utilized. Using\ua0small-angle X-ray scattering as the main characterization tool, the nanostructure of the liquid crystals as well as the anisotropy was measured. The use of imaging techniques adds an extra\ua0dimension which brings a broader view of the self-assembled structure. Microfluidic channels\ua0were used to study the mechanisms of alignment in the confined space offered by the nozzle\ua0walls and the high pressures applied in the printing process. The confined flow in the printing\ua0nozzle has different properties and constraints compared to the open flow that the extruded\ua0filament encounters in the printing platform, which was studied by in-situ 3D printing in the\ua0X-ray beam. By complementary rheological characterization, a more detailed analysis\ua0understanding of the flow behaviour was achieved and birefringence microscopy opened up\ua0the possibilities of a time-resolved study of the anisotropy in the filament. The results demonstrated the role of the shear stress in liquid crystals in confined flow,\ua0highlighting both the effect it has on the anisotropy as well as on morphological transitions\ua0in the self-assembled structures. The performed experiments also reflect on the possible\ua0causes of misalignment such as stress release and try to find the optimal parameters in the\ua0nozzle design which lead to the best alignment in terms of homogeneity in the strand and\ua0maximizing the orientation. Finally, the results also show the importance of time and\ua0environmental conditions during 3D printing, which may affect the final structure and\ua0orientation prior the fixation of the nanostructure
