An efficient preparation method, which provides wedge‐shaped cross‐section transmission electron microscopy samples, has been developed. It was then used to investigate the structure of as‐deposited cobalt multilayers on silicon substrates by rf plasma sputtering. It was found that an extended reaction takes place between Co and Si probably during the deposition. The cobalt atoms react with the silicon substrate to form an amorphous silicide layer. When the deposited layer is <3 nm thick, it entirely reacts with the substrate and can form an amorphous silicide as large as 5 nm. Above 4–5 nm thickness, growth of Co crystallites comes in competition with the formation of the amorphous silicide and limits it to 2 nm. The composition of this amorphous silicide is estimated to be Co2Si. In Co/C multilayers, the reactivity between the two materials is negligible, and the coalescence thickness of cobalt is 2–3 nm. At 2 nm, the cobalt layers are noncontinuous and very rough, whereas at 3 nm the critical thickness for crystalline nuclei coalescence has already been reached. The cobalt layers are then polycrystalline and have a reasonable roughness.