Current tissue engineering scaffolds fabricated via solvent casting and porogen leaching methods suffer from the lack of control over parameters such as interconnectivity and pore geometry, properties that are a function of the fabrication process. The progress of tissue engineering would thus benefit from the ability to design scaffolds that facilitate cell–cell interactions, and provide mass transfer characteristics necessary for good cell viability and function. In this research, we have developed two-photon laser scanning photolithography (TPLSP) for the fabrication of three-dimensional (3D) microstructured scaffolds with high resolution and fidelity. Modification of our two-photon setup allowed for a scan height of 30 mm and a scan speed of 30 mm/s, making it more amenable to scaffold fabrication. Scaffold production was adapted to computer-aided design (CAD)/computer-aided manufacturing (CAM) technology, to achieve the desired length scales from the submicron level and up. A commercially available photocurable resin that exhibited favorable ultraviolet–visible (UV–vis) transparency, cell compatibility and reproducibility in fabrication was used as the scaffold material. As a proof-of-concept, a microporous, cubic scaffold was fabricated for the purpose of hepatocyte culture. Primary hepatocytes could be uniformly seeded on these scaffolds as observed by confocal fluorescence microscopy. Albumin and urea assays demonstrated that hepatocytes cultured in the 3D scaffold maintained higher levels of liver-specific function over a period of 6 days as compared to the monolayer control. These results may be attributed to the high local concentration of soluble factors within the scaffold, which is important for maintaining the hepatocyte phenotype. Our study illustrates the potential of TPLSP as a new platform for the fabrication of designed, well-controlled, 3D microstructured tissue scaffolds.