Disclosed are methods and apparatus for inspecting a vertical semiconductor stack of a plurality of layers is disclosed. The method includes (a) on a confocal tool, repeatedly focusing an illumination beam at a plurality of focus planes at a plurality of different depths of a first vertical stack, wherein a defect is located at an unknown one of the different depths and the illumination beam has a wavelength range between about 700 nm and about 950 nm, (b) generating a plurality of in-focus images for the different depths based on in-focus output light detected from the first vertical stack at the different depths, wherein out-of-focus output light is inhibited from reaching the detector of the confocal system and inhibited from contributing to generation of the in-focus images, and (c) determining which one of the different depths at which the defect is located in the first vertical stack based on the in-focus images.