We have investigated microstructures of thermal sprayed coatings and single deposited splats using two types of ion beam milling: one is broad argon ion beam for the cross-sectioning of thermal sprayed coatings in a cross section polisher and the other is focused gallium ion beam for the cross-sectioning and transmission electron microscopy (TEM) sample preparation of single splats. The cross section of tungsten carbidecobalt (WC-Co) coatings fabricated by the polisher showed that it created a mirrored surface with minimized artifacts such as pull-outs of ceramic particles or smearings of pores which can be made by conventional metallographic preparations. A thin and locally re-thinned membrane of single nickel (Ni) splat was feasible to observe the internal interface of particle/substrate in high resolution atomic scale images. Substrate was heavily deformed by the impact of nickel particle with high kinetic and thermal energies. The particle and the substrate were intimately bonded without any voids or gaps.