We report the observation of intramolecular features on isolated silicon nanoscale clusters. Unpassivated silicon clusters are fabricated under ultrahigh vacuum (UHV) conditions, deposited onto a graphite substrate, and imaged in situ using scanning tunneling microscope (STM). We were able to resolve certain structural features of the clusters with atomic resolution. A sequence of images indicates atomic scale instability, either from diffusion or tip induced modification. The inert surface of the graphite substrate appears to allow significant mobility for atoms and small clusters, and does not strongly influence the lateral arrangement of material on the surface.