Cells in physiological 3D environments differ considerably in morphology and differentiation from those in 2D tissue culture. Naturally derived polymer systems are frequently used to study cells in 3D. These 3D matrices are complex with respect to their chemical composition, mechanical properties, and geometry. Therefore, there is a demand for well-defined 3D scaffolds to systematically investigate cell behavior in 3D. Here, fabrication techniques, materials, architectures, biochemical functionalizations, and mechanical properties of 3D scaffolds are discussed. In particular, work focusing on single cells and small cell assemblies grown in tailored synthetic 3D scaffolds fabricated by computer-based techniques are reviewed and the influence of these environments on cell behavior is evaluated.