In thermoplastic material extrusion, anisotropic properties are attributed to rapid cooling and subsequent limited diffusion time across the interface. However, the thermal history and flow-field have an additional effect on semi-crystalline polymers, resulting in changes to the crystal structure due to non-quiescent or flow-induced crystallization. These effects are most dramatic at the interface and can produce varying and asymmetric crystal morphologies in the extrudate. To quantify these effects, we use a combination of in-situ thermography and polarized light imaging to characterize cooling rate and residual stress during printing and ex-situ polarized imaging and micro-beam wide-angle x-ray scattering to characterize the non-equilibrium state of the polymer and final crystalline morphology. These measurements show that high extrusion speeds and low extrusion temperatures leave the polymer in a stretched and aligned state, which changes the nucleation density and crystal morphology at the interface between layers.