The initial reaction of AlCl₃ with a Si(111) clean surface and atomic-scale modification of the reacted surface are studied with a scanning tunneling microscope(STM). The AlC1₃ molecules dissociate upon reaction at room temperature, yielding Cl atoms around adatom sites. Chlorine atoms are observed to bond preferentially with Si center adatoms rather than Si corner adatoms, due to the difference in electronic structure. Real-time observation of the migration of adsorbed molecules around rest atoms reveals an important role of rest atoms in the initial reaction. Atomicscale modification around the adsorption sites is induced by applying a voltage pulse between the surface and the tip. Single Cl atom is extracted in both polarities. The extraction probability for a positive sample bias is higher than that for a negative one. It is also found that the extraction probability increases with tunneling conductance. The manipulation and dissociation of adsorbed molecules are also demonstrated.