e-beam evaporation while keeping the substrate at room temperature will result in a nanocrystalline structure. The microstructure will depend on the process conditions, such as the deposition rate, but typically grain sizes are larger than the thickness.
If the difference between nanocrystalline and amorphous structures is important for your application, there are routes you can consider such as Ar plasma to amorphize the film but it requires optimization as it can cause sputtering, intermixing with the substrate, Ar implantation and an assortment of defects