Volume correlative light and electron microscopy (vCLEM) enables ultrastructural analysis of rare cellular events. Here, we present a protocol for targeting virus-containing amphisomes in eukaryotic cells with vCLEM. We describe steps for identifying target cells using confocal fluorescence microscopy, preparing and mounting samples for focused ion beam-scanning electron microscopy (FIB-SEM), relocating the target cells and FIB-SEM stack acquisition, and correlation of volume light and electron microscopy data for 3D modeling. This protocol is optimized for imaging adherent cultured cells. For complete details on the use and execution of this protocol, please refer to Schmidt et al.(1).