Coarsening dynamics of Ge/Si(100) nanostructures were monitored using real-time, elevated temperature scanning tunneling microscopy. Gas-source molecular beam epitaxy from digermane at 0.2 ML / min onto Si(100) at temperatures near 500 °C produced mixed hut and pyramid cluster ensembles. The width of the most elongated rectangular-based hut clusters is always less than the side length of square-based pyramid clusters for island ensembles grown using these conditions. This suggests that pyramid elongation to form hut clusters occurred at early growth stages for some smaller clusters. Growth temperature annealing revealed that pyramid clusters are more stable than narrow hut clusters with larger volumes. These larger volume huts decay by reducing their length at constant width, finally becoming small pyramids. These pyramids, which are smaller than those which never elongated to form huts, are less stable and consequently dissolve. Atomistic elastic modeling confirms that hut clusters less efficiently store elastic energy than pyramid clusters which explains our observations. Large (> 1μm diameter), low chemical potential clusters deplete the surface of Ge adatoms as evidenced by the existence of denuded zones devoid of smaller clusters. These large clusters are responsible for the decrease in total island volume in the STM field of view during the anneal.