Herein, we invesgate the consequence of local voltage pulses on the adsorption state of single indigo molecules on the Cu(111) surface as well as on the atomic structure underneath the molecule. With a scanning tunneling microscope, at 5 K, intact molecules are imaged as two lobes corresponding to the electron density of each indoxyl moiety of the molecule which are connected by a carbon double bond. Then, two short successive voltage pulses with the tip placed above the molecule generate irreversible modifications, as revealed by consecutive scanning tunneling microscopy (STM) imaging. Density-functional theory calculations coupled to STM image calculations indicate the creation of a double surface vacancy of copper surface atoms below the oxygen atom of the indigo molecule as the most plausible scenario. These extracted copper atoms are stabilized as adatoms by the indigo oxygens, oxidizing each copper adatom to 0.32 electron.