We describe two examples of application focusing on first-principles molecular dynamics as an effective tool to unravel the atomic-scale structure of condensed-matter systems. The first application is on disordered network-forming materials and the second is on silicon-doped fullerenes. We show that an accurate modelling of interatomic forces based on density functional theory, when combined with an account of the temperature evolution, is an unavoidable prerequisite for analyzing and interpreting experimental results on a quantitative basis. In the case of disordered systems, we describe the basic structural features of amorphous GeSe4 and highlight the predominant chemical order in this system. The effect of adding or removing an electron charge on the stability of Si-doped fullerenes is exemplified by considering the finite temperature evolution of heterofullerenes.