Silicon-on-nothing (SON) [1] and germanium-on-nothing (GON) [2] are self-assembled membrane structures over cavities resulting from atomic migration towards minimization of surface energy upon high temperature annealing. In general, SON and GON related researches seek for saturated annealed structures of which membrane or cavity shapes do not change further. To obtain such saturated SON or GON structures, samples prepared are annealed sufficiently in a favorable condition thus self-assembled surfaces tend to be extremely uniform and smooth. For sample inspection or process monitoring, self-assembled samples are cleaved and examined with a scanning electron microscope. Due to the absence of appreciable surface roughness, cross-sectional images obtained through the destructive test cannot be correlated with the surface topographic features. In this study, we anneal hole-arrays patterned silicon and germanium wafers in a time-controlled manner to stop before saturation. After this time-controlled annealing, surface atomic force micrographs (AFMs) and cross-section scanning electron micrographs (SEMs) are obtained before and after the sample cleaving, respectively. Obtained surface AFMs and cross-section SEMs are thoroughly analyzed to find out meaningful correlations.