Semiconductor device assemblies having features that are used to align semiconductor dies, and associated systems and methods, are disclose herein. In some embodiments, a semiconductor device assembly includes substrate that has a top surface and an alignment structure at the top surface. A first die is disposed over the top surface of the substrate, and the first die has a first channel that extends between a top side and a bottom side of the first die. The first channel is vertically aligned with and exposes the alignment structure at the top surface of the substrate.