Liquids and solids are two fundamental states of matter. However, due to the lack of direct experimental determination, our understanding of the 3D atomic structure of liquids and amorphous solids remained speculative. Here we advance atomic electron tomography to determine for the first time the 3D atomic positions in monatomic amorphous materials, including a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into networks that extend to medium-range scale. Molecular dynamic simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic amorphous liquids, which rapidly grow in size and form icosahedra during the quench from the liquid state to glass state. The experimental method and results are expected to advance the study of the amorphous-crystalline phase transition and glass transition at the single-atom level.