An atomic force microscope (AFM) under noncontact and nearcontact regions operated at room-temperature (RT) in ultrahigh vacuum, is used as a tool for topography-based atomic discrimination and lateral atomic manipulations of two intermixed atomic species on semiconductor surfaces. Noncontact AFM topography can give height difference between two intermixed atomic species. Therefore, noncontact AFM topography is a kind of atom selective image and hence can serve for atomic discrimination in simple cases. Besides, site-specific force curves provide the chemical covalent bonding forces between the tip apex and the atoms at the surface. Here, we introduced both examples related to topography-based atomic discrimination using selected Sn and Si adatoms in Sn/Si(111)-(√3×√3) surface. Recently, under nearcontact region, we found a lateral atom-interchange manipulation phenomenon at RT in Sn/Ge(111)-c(2×8) intermixed sample. This phenomenon can interchange an embedded Sn atom with a neighbor Ge atom at RT. Using the vector scan method under nearcontact region, we constructed “Atom Inlay”, that is, atom letters “Sn” consisted of 19 Sn atoms embedded in Ge(111)-c(2×8) substrate. Using these methods, now we can assemble compound semiconductor nanostructures atom-by-atom. Keywords: Atom-by-atom assembly, Atomic discrimination, Atomic force microscopy, Site-specific force spectroscopy, Lateral atom manipulation, Atom-interchange manipulation