Micro scale features are fabricated on Si (100) surfaces using lithographic techniques and then thermally processed in an ultra high vacuum (UHV) environment. Samples are flash heated at 1200 °C and further annealed at 1050 °C for 18 hours. The surface morphology was examined using an atomic force microscopy (AFM). The process resulted in the formation of symmetric, reproducible step-terrace patterns with very wide atomically flat regions exhibiting highly reproducible step-terrace morphology. 25 µm lithographically patterned cells spontaneously transform into a symmetric formation marked by step bunches pinned by pyramidal structures separated by wide atomic terraces. The pyramidal features are visible using a conventional optical microscope and are to be used as fiducial marks to locate nanoscale features fabricated on the atomically flat terraces.