Perpendicular shape anisotropy (PSA) and double magnetic tunnel junctions (DMTJs) offer practical solutions to downscale spin-transfer-torque Magnetic Random-Access Memory (STT-MRAM) beyond 20 nm technology nodes, while retaining their thermal stability and reducing critical currents applied. However, as these modern devices become smaller and three-dimensionally (3D) complex, our understanding of their functional magnetic behavior is often indirect, relying on magnetoresistance measurements and micromagnetic modeling. In this paper, we review recent work that was performed on these structures using a range of advanced electron microscopy techniques, focusing on aspects specific to the 3D and nanoscale nature of such elements. We present the methodology for the systematic transfer of individual SST-MRAM nano-pillars from large-scale arrays to image their magnetic configurations directly using off-axis electron holography. We show that improved phase sensitivity through stacking of electron holograms can be used to image subtle variations in DMTJs and the thermal stability of in situ heating. The experimental practicalities, benefits, and limits of using electron holography for the analysis of MRAM devices are discussed, unlocking practical pathways for direct imaging of the functional magnetic performance of these systems with high spatial resolution and sensitivity. (C) 2022 Author(s).