A method of selecting molecules embedded in nanodroplets (clusters) of superfluid helium is proposed, which is based on the selective vibrational excitation of embedded molecules by intense IR laser radiation. This action leads to a significant decrease in size of the excited clusters, after which these clusters are separated with respect to size via scattering of the cluster beam on a crossing atomic beam. The method is described in detail and the possibility of selecting SF6 molecules in liquid helium nanodroplets using the excitation by CO2 laser radiation and the angular separation via scattering on a xenon atomic beam is demonstrated. The results show that, by using this technique, it is possible to separate molecules with respect to isotope (element) composition. Advantages and drawbacks of the method are analyzed.