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A 3D printing fused filament fabrication (FFF) approach has been implemented for the creation of microstructures having an internal 3D microstructure geometry. These objects were produced without any sacrificial structures or additional support materials, just by precisely tuning the nozzle heating, fan cooling and translation velocity parameters. The manufactured microporous structures out of polylactic acid (PLA) had fully controllable porosity (20%–60%) and consisted of desired volume pores (~0.056 μm³). The prepared scaffolds showed biocompatibility and were suitable for the primary stem cell growth. In addition, direct laser writing (DLW) ablation was employed to modify the surfaces of the PLA structures, drill holes, as well as shape the outer geometries of the created objects. The proposed combination of FFF printing with DLW offers successful fabrication of 3D microporous structures with functionalization capabilities, such as the modification of surfaces, the generation of grooves and microholes and cutting out precisely shaped structures (micro-arrows, micro-gears). The produced structures could serve as biomedical templates for cell culturing, as well as biodegradable implants for tissue engineering. The additional micro-architecture is important in connection with the cell types used for the intention of cell growing. Moreover, we show that surface roughness can be modified at the nanoscale by immersion into an acetone bath, thus increasing the hydrophilicity. The approach is not limited to biomedical applications, it could be employed for the manufacturing of bioresorbable 3D microfluidic and micromechanic structures. Full article