A straightforward approach allowing three-dimensional (3D) visualization of subsurface deformation beneath nanoindents using reconstructed cross-sectional transmission electron microscopy (TEM) data is demonstrated. This approach relies on generating an array of nanoindents, extracting a thin (<200 nm) cross section using a focused ion beam (FIB) and imaging with a transmission electron microscope. By rotating the orientation of the FIB cross section with respect to the array of nanoindents at the optimal angle, it is guaranteed that a different section of each nanoindent's subsurface plastic zone is contained within the final cross section. Subsequently, TEM images corresponding to different sections are reconstructed into a 3D image of a representative nanoindentation plastic zone. This approach can be extended to any array of nominally identical features that can be patterned with regular spacing and included in a single FIB cross section. It was also found to significantly enhance the throughput of preparing routine site-specific TEM samples, even when 3D visualization is not necessary. In this article, the approach is applied to visualize the plastic zones beneath nanoindents in GaAs (001), for loads of 50–1000 µN.