The invention encompasses a method of forming a rugged silicon-containing surface. The clock data recovery circuit has an output signal of B bits and comprises a sampler, a phase region decision circuit, a phase status register and a multiplexer. Then a second stack comprised of an underlayer, a non-photosensitive Si-containing layer, an ARC, and a photoresist are formed on the first stack. The system then estimates one or more of the stress factors based on the classification result.