Molecular Dynamics (MD) simulation has been utilized for the investigation of surface retreatment of copper and iron oxides during laser irradiation of their suspensions to investigate the possible chemical phase formation during the PLIL process. In the present investigation, it is tried to calculate the energies for various probable surface ionizations and functionalization of nanoparticles (NPs) in the ionic liquid (IL). Copper (Cu), CuO, and Fe3O4 NPs are functionalized, transferred, and stabilized with the organic ligands, in different polar and nonpolar organic solvents. The atomic and molecular functionalization of raw NPs surfaces in IL solvent has an undeniable effect on the final product. The aim of this study is to find out the surface functionalization of the Cu-Fe-O ternary system in ILs for the prediction of compounds that are preferred to be composed by PLIL. MD calculations showed the favorable interactions between IL anions instead of IL cations. This suggests a Cu-Fe-O interaction with anionic Cun stabilization in ILs which is a reason for the formation of the copper spinel phase (CuFe2O4). However, there are minor differences between surface functionalization in various ILs i.e. acetyl acetate, and toluene. Moreover, there is a reasonable harmony by the comparison between MD calculations and the experimental results.