We report the fabrication of connected open structures from close-packed colloidal crystals by hyperthermal neutral beam etching. Colloidal crystal films of polystyrene microspheres were prepared by a vertical deposition method. Exposure of the colloidal crystal films to hyperthermal neutral beam made isolated microspheres in the face-centered cubic lattice, each of which was connected with its twelve nearest neighbors through very thin cylinders. Due to the charge neutrality of impinging gas molecules of the hyperthermal neutral beam, the spherical shape of polymer microspheres was almost maintained during the etching process. The Bragg reflection peaks were modulated by the etched volume of colloidal crystals. Finally, the inverse structures of such open structures were replicated by a simple room-temperature chemical vapor deposition and subsequently burning out polymer template spheres.