Using an energy filter in transmission electron microscopy has enabled elemental mapping at the atomic scale and improved the precision of structural determination by gating inelastic and elastic imaging electrons, respectively. Here, we use an energy filter in ultrafast electron microscopy to enhance the temporal resolution toward the domain of atomic motion. Visualizing transient structures with femtosecond temporal precision was achieved by selecting imaging electrons in a narrow energy distribution from dense chirped photoelectron packets with broad longitudinal momentum distributions and thus typically exhibiting picosecond durations. In this study, the heterogeneous ultrafast phase transitions of vanadium dioxide (VO ₂ ) nanoparticles, a representative strongly correlated system, were filmed and attributed to the emergence of a transient, low-symmetry metallic phase caused by different local strains. Our approach enables electron microscopy to access the time scale of elementary nuclear motion to visualize the onset of the structural dynamics of matter at the nanoscale.