A method and apparatus to characterize a shape of an isomeric form of a sample comprised of a molecule or a cluster of molecules. The method includes raising an electron of the sample to a Rydberg state having an orbital diameter sufficient to encompass at least a portion of the sample; further raising the electron to an ionization state and correlating the energy required to transition from the Rydberg state to the ionization state with the three dimensional structure of the sample. In a preferred embodiment raising the electron to the Rydberg state includes raising the electron to a first Rydberg state Ry.sub.1, and then raising the electron to a second Rydberg state Ry.sub.2. Further raising the electron to the ionization state includes raising the electron from the Ry.sub.2 state to the ionization state using optical excitation, and correlating the energy considers at least a wavelength of the optical excitation. Also disclosed are method and apparatus that use the Rydberg states to separate at least one isomeric form of a sample from other isomeric forms of the sample, where the sample is comprised of a molecule or a cluster of molecules.