Fused deposition modelling (FDM) is an additive manufacturing technique widely used for rapid prototyping. This method facilitates the creation of parts with intricate geometries, making it suitable for advanced applications in fields such as tissue engineering, aerospace, and electronics. Despite its advantages, FDM often results in the formation of voids between the deposited filaments, which can compromise mechanical properties. However, in some cases, such as the design of scaffolds for bone regeneration, increased porosity can be advantageous as it allows for better permeability. On the other hand, the introduction of nano-additives into the FDM material enhances design flexibility and can significantly improve the mechanical properties. Therefore, modelling FDM-produced components involves complexities at two different scales: nanoscales and microscales. Material deformation is primarily influenced by atomic-scale phenomena, especially with nanoscopic constituents, whereas the distribution of nano-reinforcements and FDM-induced heterogeneities lies at the microscale. This work presents multiscale modelling that bridges the nano and microscales to predict the mechanical properties of FDM-manufactured components. At the nanoscale, molecular dynamic simulations unravel the atomistic intricacies that dictate the behaviour of the base material containing nanoscopic reinforcements. Simulations are conducted on polylactic acid (PLA) and PLA reinforced with silver nanoparticles, with the properties derived from MD simulations transferred to the microscale model. At the microscale, non-classical micropolar theory is utilised, which can account for materials’ heterogeneity through internal scale parameters while avoiding direct discretization. The developed mechanical model offers a comprehensive framework for designing 3D-printed PLA nanocomposites with tailored mechanical properties.