Three dimensional models of insect specimens offer the potential for a variety of research applications, including taking morphological and trait measurements of insects and automated species identification. Yet high-quality 3d models are challenging to create because of the specimens’ small size. Here we overcome this challenge by creating 3d models using focal stacking to take high-resolution images of bee specimens. Sets of 3d images are processed using Zerene Stacker and Photoshop, and the 3d models are created using Agisoft Metashape. Our protocol can be used for both larger insect specimens, like bumble bees and carpenter bees, and small- and medium-sized specimens, such as mason and sweat bees. This protocol is being used by members of the Cheadle Center for Biodiversity and Ecological Restoration at the University of California, Santa Barbara, and is based on a protocol developed by members of the Big-Bee project.