Three-dimensional (3D) scaffolds composed of poly(epsilon-caprolactone) and gelatin nanofibers were fabricated by a combination of electrospinning and modified gas-foaming. Arrayed holes throughout the scaffold were created using a punch under cryo conditions. The crosslinking with glutaraldehyde vapor improved the water stability of the scaffolds. Cell spheroids of green fluorescent protein-labeled human dermal fibroblasts were prepared and seeded into the holes. It was found that the fibroblasts adhered well on the surface of nanofibers and migrated into the scaffolds due to the porous structures. The 3D nanofiber scaffolds may hold great potential for engineering tissue constructs for various applications.