We have achieved pattern transfer from a biomolecular nanomask (bionanomask) to a crystalline Si substrate using inductively coupled plasma etching. This nanopatterning makes use of an intermediate transfer layer (ITL) between the masks and the substrate. The ITL is a layer of a resist-like material into which the bionanomask pattern is transferred before it is then transferred to the substrate. We report a method for using bionanomasks deployed on an ITL of ultrathin (< 10 nm) nitrocellulose to pattern a Si(100) substrate with either a two-dimensionally ordered array of 10-nm-diam holes or alternatively a two-dimensionally ordered array of 10-nm-diam metal dots. Both arrays possess hexagonal symmetry and a lattice constant of 22 nm. In the case of nanodot array fabrication, the ITL thus facilitates the direct replication of the inverse pattern of the bionanomask in the form of ordered metal nanodots without the need for adsorbate surface diffusion and nucleation steps.