In this paper we demonstrate a facile and efficient way to fabricate poly(dimethylsiloxane) (PDMS) molds with hexagonal non-close-packed (ncp) arrangements of microwells by casting PDMS prepolymer onto two-dimensional (2D) ncp colloidal crystals. The templates of the 2D ncp colloidal crystals were fabricated via coupling lift-up soft lithography and solvent-swelling. We found that the depths of the microwells together with the lattice spacing can be adjusted by the sphere interstices and chemical composition of the 2D ncp colloidal crystals. The relationship of the surface character of the templates with the depths of the microwells can be explained by the wetting behavior of PDMS prepolymer on the rough surface. Contact angle measurements are consistent with the experimental results of the microwells in depth and agree well with the Cassie-Baxter theory. There are at least three advantages of the approach. First, the depth and distance of the microwells can be controlled. Second, PDMS molds can be easily peeled from the surfaces of the templates, which results in reusing the original templates to make new molds. Third, this method can be applied to other materials, such as photopolymerizable resin or thermosetting resin. The potential application of the microwells is as microlenses to make a pattern or as microvials in bioanalytical techniques.