Three-dimensional epoxy scaffolds with abundant active epoxy groups on surfaces were fabricated through UV-Assisted direct-write manufacturing process. The prepared scaffolds composed of cylindrical filaments (diameter ∼100 μm) were aminated by reacting the epoxy groups with 1,3-diamino-propane. The resulting aminated scaffolds were subsequently biotinylated and then successfully applied to immobilize biotinylated nanoclay conjugates via a specific, strong and rapid binding of biotin and streptavidin. In another approach, the same amount of nanoclays was properly dispersed in epoxy by three-roll mill machine inducing high shear mixing. The nanoclay-epoxy filaments were then deposited by a computerized-control robot in a 3D micro structure scaffold form. Tensile mechanical tests were performed with a dynamic mechanical analysis (DMA) using a film tension clamp on three microstructures: nanoclay-epoxy scaffolds, aminated-biotinylated nanoclays coated on unloaded epoxy scaffolds and finally unloaded epoxy scaffolds (used as a reference). DMA tensile measurements indicated a slight improvement in modulus (by ∼5%), but significant increase in strength (by ∼24%), fracture strain (by ∼21%) and fracture energy (by ∼38%) by introducing biotin-streptavidin strong bonds among epoxy scaffolds and nanoclays in comparison with those of mixed nanoclay-epoxy scaffolds. These mechanical improvements are attributed to the strong biotin and streptavidin bonds between the epoxy scaffolds and nanoclays.