ABSTRACT Morphological analysis of fine structures on small insects is often labor intensive, scale‐limited, and biased by sampling or organismal life history. We used a pixel classification machine‐learning workflow with the open source programs Ilastik and Fiji to identify and quantify microtrichia in semiaquatic shore flies (Ephydridae). This methodology semi‐automates quantification of hairs by counting objects or groups of class‐assigned pixels and determining their percent coverage at a given magnification using scanning electron micrographs. Our results are consistent with manual counts, with Paracoenia species that tolerate hot springs having more hairs than less aquatic Parydra . However, Paracoenia hairs tend to be shorter, and the percent coverage of microtrichia per unit surface area did not differentiate species except for the anterior thoracic spiracle. Our workflow is adaptable for use in other taxonomic groups or beyond the quantification of hairs, with the upper limits of applicability determined by overlap in the feature of interest. As molecular datasets continue to grow and proliferate in the multi‐omics age, efficient morphological workflows become even more critical to allowing proportionally robust, complementary biological inferences grounded in phenotypic data.