The use of optical microcavities, high-Q resonators and slow-light structures as tools for detecting molecules and probing conformations and measuring polarizability and anisotropy of molecules and molecular assemblies using a pump-probe approach is described. Resonances are excited simultaneously or sequentially with pump and probe beams coupled to the same microcavity, so that a pump beam wavelength can be chosen to interact with molecules adsorbed to the microcavity surface, whereas a probe beam wavelength can be chosen to non-invasively measure pump-induced perturbations. The induced perturbations are manifest due to changes of resonance conditions and measured from changes in transfer characteristics or from changes of the scattering spectra of a microcavity-waveguide system. The perturbations induced by the pump beam may be due to polarizability changes, changes in molecular conformation, breakage or formation of chemical bonds, triggering of excited states, and formation of new chemical species.