When bulk materials join at atomic scale, new and unexpected physical regimes can emerge due to nano-scale effects which arise from newly imposed quantum-mechanical boundary conditions at interfaces. To discover and investigate these physical regimes, knowing what the atoms are, and how they are arranged at interfaces is essential. Over the last few decades, electron microscopy and spectroscopy have become indispensable tools to study nano-scale effects because they provide structural as well as electronic, chemical, and optical information at atomic scale. In this thesis, I used electron energy-loss spectroscopy (EELS) as a primary experimental tool to explore how a nano-scale interfacial chemistry and geometry determine the overall properties of nano-scale systems. By investigating the inelastic scattering events between the incident probe electrons and the nano-scale systems, EELS gives site-specific electronic, chemical, and optical information about the systems. Three topics were investigated with EELS in detail: modifications in the electronic structure of carbon nanotubes in contact with islanding and wetting metals, effects of barrier/electrode interfacial chemistry on tunneling magnetoresistance in sputtered MgObased magnetic tunnel junctions, and nanometer-scale imaging of and finite size effects on photonic modes of diamond and silicon photonic structures. In the carbon nanotube project, I used electron tomography to reconstruct the threedimensional contact geometry between carbon nanotubes and metal contacts, which showed that carbon nanotubes were deformed by islanding metals, implying that the electronic band structure of a nanotube could be modified by making contact to a metal. EELS measurements on carbon nanotubes deformed by islanding metals showed differences in the C-K fine structure between pristine and deformed regions of the nanotubes, which suggested that the band structure of the nanotubes was modified upon deformation. In the MgO-based magnetic tunnel junction project, core-loss spectroscopic imaging of the MgO/B-alloy electrode interface showed a clear presence of B as B oxide in the MgO layer due to the inevitable oxidation of the base electrode during radio frequency sputtering of MgO. Subsequent annealing of the magnetic tunnel junctions resulted in a hybrid Mg-B-O layer which still produced high tunnel magnetoresistance and low resistance-area product in thin (~ 1 nm) Mg-B-O barrier regime, making the thermally stable Mg-B-O a technologically relevant barrier material for magnetic tunnel junctions. Lastly in the diamond and silicon photonic structure project, I used monochromated EELS in the low energy-loss region to probe optical modes of diamond and silicon photonic structures at nanometer resolution, made possible by retardation effects where emitted radiation by relativistic electrons acted as a virtual light source, coupling to the photonic modes of the diamond and silicon photonic structures. In particular, spatial distributions of the photonic modes and damping of the modes due to finite size effects were investigated in detail. This thesis provides background information on core- and low-loss EELS and discusses experimental set-ups and results for each project.