Meteorites and Interplanetary Dust Particles (IDPs) are supposed to originate from asteroids and comets, sampling the most primitive bodies in the Solar System. They contain abundant carbonaceous material. Some of this, mostly insoluble organic matter (IOM), likely originated in the protosolar molecular cloud, based on spectral properties and H and N isotope characteristics. Together with cometary material returned with the Stardust mission, these samples provide a benchmark for models aiming to understand organic chemistry in the interstellar medium, as well as for mechanisms that secured the survival of these fragile molecules during Solar System formation. The carrier molecules of the isotope anomalies are largely unknown, although amorphous carbonaceous spheres, so-called nanoglobules, have been identified as carriers. We are using Secondary Ion Mass Spectrometry to identify isotopically anomalous material in meteoritic IOM and IDPs at a ~100-200 nm scale. Organics of most likely interstellar origin are then extracted with the Focused-Ion-Beam technique and prepared for synchrotron X-ray and Transmission Electron Microscopy. These experiments yield information on the character of the H- and N-bearing interstellar molecules: While the association of H and N isotope anomalies with nanoglobules could be confirmed, we have also identified amorphous, micron-sized monolithic grains. D-enrichments in meteoritic IOM appear not to be systematically associated with any specific functional groups, whereas 15N-rich material can be related to imine and nitrile functionality. The large 15N- enrichments observed here (δ15N > 1000 %) cannot be reconciled with models using interstellar ammonia ice reactions, and hence, provide new constraints for understanding the chemistry in cold interstellar clouds.