Amorphous silicon films prepared by electron-beam evaporation have systematically and substantially greater atomic density for higher thickness, higher growth temperature, and slower deposition rate, reaching the density of crystalline Si when films of thickness greater than ∼300 nm are grown at 425 °C and at <1 Å/s. A combination of spectroscopic techniques provide insight into atomic disorder, local strains, dangling bonds, and nanovoids. Electron diffraction shows that the short-range order of the amorphous silicon is similar at all growth temperatures, but fluctuation electron microscopy shows that films grown above room temperature show a form of medium-range order not previously observed in amorphous silicon. Atomic disorder and local strain obtained from Raman spectroscopy are reduced with increasing growth temperature and show a nonmonotonic dependence on thickness. Dangling bond density decreases with increasing growth temperature and is only mildly dependent on thickness. Positron annihilation Doppler broadening spectroscopy and electron energy loss spectroscopy show that nanovoids, and not density variations within the network, are responsible for reduced atomic density. Specific heat and mechanical loss measurements, which quantify the density of tunneling two-level systems, in combination with the structural data, suggest that two-level systems in amorphous silicon films are associated with nanovoids and their surroundings, which are in essence loosely bonded regions where atoms are less constrained.