A novel method of forming large atomically flat areas is described in which a crystalline substrate having a stepped surface is exposed to a vapor of another material to deposit a material onto the substrate, which material under appropriate conditions self arranges to form 3D islands across the substrate surface. These islands are atomically flat at their top surface, and conform to the stepped surface of the substrate below at the island-substrate interface. Thereafter, the deposited materials are etched away, in the etch process the atomically flat surface areas of the islands transferred to the underlying substrate. Thereafter the substrate may be cleaned and annealed to remove any remaining unwanted contaminants, and eliminate any residual defects that may have remained in the substrate surface as a result of pre-existing imperfections of the substrate.