In this article, we discuss the recent use of the high-resolution dynamic atomic force microscopy (DAFM) in mapping the nano-scale dynamical structural heterogeneity in thin film metallic-glasses (TFMGs). Our focus is laid on the major factors which can influence the structural contrast in the DAFM images, such as tip radius, free-amplitude, set-point amplitude and surface roughness. Finally, through a comparative study of different TFMGs and single-crystal silicon, we demonstrate that the DAFM technique is effective in distinguishing different nanostructures through their energy dissipation spectra. •Obtaining the structural image requires adjusting the free amplitude.•Obtaining the structural image requires adjusting the set-point amplitude.•Obtaining the structural image demands a smooth surface.•The obtained structural image is tip radius dependent.•The obtained structural images can distinguish different nanostructures.