Three-dimensional (3D) visualization of complex embedded nanopore networks in silicon requires expensive machinery and tedious sample preparation procedures such as electron tomography, also known as 3D transmission electron microscopy. In this article, we report a new, fast, powerful, and low-cost three-dimensional imaging technique with sub-5 nm resolution. This new imaging method is applied to metal-assisted chemically etched monocrystalline Si to demonstrate its capabilities. The AFEI (atomic layer deposition-fill-etch-imaging) technique consists of three simple process steps that are available in most material research settings. First the porous substrate is conformally coated with an atomic layer deposition (ALD) metal oxide layer. ALD is able to penetrate deep into complex, high aspect ratio pores, as it is a sequential gas-phase deposition process. Next, the cross-section of the ALD-filled porous Si substrate is etched with high-density fluorine-based plasma processing, which yields very high selectivity toward Si (e.g., >400:1 for Si:ZnO). This step removes the bulk Si and exposes the metal oxide structures grown inside the pores. In the last step, the sample cross-section is examined using a standard scanning electron microscope at various angles, which allows precise imaging of hidden features and reconstruction of a 3D model of the embedded pore network.