A method of separating isotopes from polyatomic molecules, in particular <13>C from trifluoromethane HCF3, by applying to the polyatomic molecules in the gas phase infrared laser beams of different frequencies to produce multiphoton dissociation and reaction resulting in separable isotopes. The first laser has a frequency and a energy fluence to produce vibrationally preexcited molecules enriched in the desired isotope, for instance <13>C. The second laser has a frequency and energy fluence to selectively induce dissociation of the vibrationally preexcited molecules by infrared multiphoton excitation. The product of the pressure of the molecules and the time-delay of the second laser pulse relative to the first allows collisional vibrational deactivation of a substantial amount of the vibrationally preexcited molecules containing non-desired isotope(s), like <12>C, before dissociation of the vibrationally excited molecules occurs, while there is no significant collisional vibrational deactivation of preexcited molecules containing the desired isotope, like <13>C. The dissociation products are hence highly enriched in the desired isotope. The laser beams are collimated or slightly diverging or slightly converging beams of low fluence (≤5 J/cm<2>) substantially overlapping with one another.