Laser irradiated Si(100) surfaces were studied with an ultrahigh vacuum scanning tunneling microscopy system, Our observations indicate that only the dimerized outermost atomic layer is removed if the laser fluence is below the melting threshold at photon energy larger than the band gap. The newly exposed layer, surprisingly, did not have a dimerized atomic structure, but rather, resembled that of a bulk-terminated structure. The uncovered layer remained atomically smooth (no vacancies) even after 90% of the outermost layer was removed. A possible explanation of these observations is that atom removal occurs by a preferential breakage of the atomic bonds in defect sites. When the laser fluence was increased to levels above the melting threshold, extensive surface roughening occurs.