In spite of the rather large use of the fused deposition modeling (FDM) technique for the fabrication of scaffolds, no studies are reported in the literature that optimize the geometry of such scaffold types based on mechanobiological criteria. We implemented a mechanobiology-based optimization algorithm to determine the optimal distance between the strands in cylindrical scaffolds subjected to compression. The optimized scaffolds were then 3D printed with the FDM technique and successively measured. We found that the difference between the optimized distances and the average measured ones never exceeded 8.27% of the optimized distance. However, we found that large fabrication errors are made on the filament diameter when the filament diameter to be realized differs significantly with respect to the diameter of the nozzle utilized for the extrusion. This feasibility study demonstrated that the FDM technique is suitable to build accurate scaffold samples only in the cases where the strand diameter is close to the nozzle diameter. Conversely, when a large difference exists, large fabrication errors can be committed on the diameter of the filaments. In general, the scaffolds realized with the FDM technique were predicted to stimulate the formation of amounts of bone smaller than those that can be obtained with other regular beam-based scaffolds.