We report the reaction dynamics of cobalt phthalocyanine (CoPc) molecules with Bi-line structures (BLSs) on a Si(100) surface, investigated using scanning tunneling microscopy (STM). When CoPc molecules were deposited on a Si(100) surface with BLSs at room temperature, single-spot protrusions were observed in the STM image instead of four-spot images corresponding to CoPc’s flat molecular struc...