The Morley Nelson Snake River Birds of Prey National Conservation Area (NCA) provides breeding sites for raptors in southwestern Idaho. Biologists have been mapping occupied Golden Eagle nest locations in the NCA since the 1960s, but the steep cliffs used by raptors as nesting sites are difficult to represent on traditional 2D maps. This study used uncrewed aircraft systems (UAS) equipped with multispectral sensors to collect imagery over Crater Rings National Natural Landmark within the NCA. Using different sensor systems, UAS platforms, and flight patterns, we investigated the most effective methods to collect imagery to create high quality 3D mapping products. Our findings show that using a façade style flight pattern paired with an obliquely faced red-green-blue camera provided digital maps with few holes and gaps over the cliff faces. We also developed a nest site suitability model using topographic parameters of slope, solar radiation, terrain ruggedness index, and height above the crater floor. The suitability model corresponded to current and historical nesting locations. These maps pinpoint areas important for nesting raptors and have the potential to investigate how changing climate and increasing invasive plants are influencing the availability of nest sites.