Dense, periodic arrays of holes and troughs have been fabricated in silicon, silicon nitride, and germanium. The holes are approximately 20 nanometers (nm) wide, 20 nm deep, spaced 40 nm apart, and uniformly patterned with 3X10(12) holes on a three inch wafer. To access this length scale, self-assembling resists were synthesized to produce either a layer of hexagonally ordered polyisoprene (PI) spheres or parallel cylinders of polybutadiene (PB) in a polystyrene (PS) matrix. The PI spheres or PB cylinders were then degraded and removed with ozone to produce a PS mask for pattern transfer by fluorine-based reactive ion etching. A PS mask of spherical voids was used to fabricate a lattice of holes and a mask of cylindrical voids was used to produce parallel troughs. This technique accesses a length scale difficult to produce by conventional lithography and opens a route for the patterning of surfaces via self-assembly.