Hexagonally arrayed structures of colloidal crystals with uniform surface are a good candidate for master molds to be used in soft lithography. Here, the fabrication of periodically arrayed nanostructures using poly(dimethylsiloxane) (PDMS) molds based on three-dimensionally (3D) ordered colloidal crystals is reported. A robust, high-quality 3D colloidal-crystal master molds is prepared using the colloidal suspension containing a water-soluble polymer. The surface patterns of the 3D colloidal crystals can then be transferred onto a polymer film via soft lithography, by means of the replication of the surface pattern with PDMS. Various hexagonally arrayed nanostructure patterns can be fabricated, including close-packed and non-close-packed 2D arrays and honeycomb structures by the structural modification of the 3D colloidal-crystal templates. The replicated hexagonally arrayed structures can also be used as templates for producing colloidal crystals with 2D superlattices.