A method of aligning a plurality of empty-spaced buried patterns formed in semiconductor monocrystalline substrates is disclosed. In an exemplary embodiment, high-temperature metal marks are formed to include a conductive material having a melting temperature higher than an annealing temperature used to form such empty-spaced buried patterns. The high-temperature metal marks are formed prior to the formation of the empty-spaced buried patterns formed in a monocrystalline substrate, so that the empty-space buried patterns are aligned to the marks. Subsequent semiconductor structures that are formed as part of desired semiconductor devices can be also aligned to the marks.