Résumé : Inter-filament voids are critical defects in fused deposition modelling, leading to stress concentrations with undesired effects on the strength of the printed part. This work presents a novel methodology for the computational analysis of the mechanical behaviour of 3D printed materials incorporating these voids by exploiting computed tomography scans to automatically generate conformal finite element (FE) meshes with user control on the geometrical details accounted for in the model. This is achieved through an advanced curvature-based local smoothing algorithm, which preserves mechanically relevant morphological characteristics while reducing computational complexity and filtering out irrelevant geometrical features. The proposed approach is applied to 3D printed short carbon fibre reinforced polyether ether ketone (SCFR PEEK) samples subjected to realistic loading conditions. Results show inter-filament void induced stress concentrations and the occurrence of plastic events in the microstructural volume, leading to guidelines for choosing the appropriate level of the geometrical details and features to embark in the FE model.