A recent study identified topography (land surface elevation above sea level) as an important input dataset (feature) for predicting the location of hydrothermal systems in the Great Basin in Nevada. Yet, topography is generally a result of more than one geological process and may consequently contain multiple distinct signals. For example, the geologic evolution of the Great Basin has produced both crustal thickening (i.e., regional-scale trends in elevation) and thinning via Basin and Range extensional faulting (i.e., valley-scale topographic relief). We postulate that these geologic processes may affect the occurrence of hydrothermal systems differently. Therefore, we separate the regional trend from the valley-scale signal in the Great Basin, and then use them separately to evaluate the importance of each as predictors for hydrothermal favorability. Our prior work applying supervised machine learning (ML) using the data from the Nevada Machine Learning Project demonstrated that employing a training strategy that randomly selects negative training sites produces better performing models for predicting hydrothermal favorability than a training strategy that uses expert-selected negatives. The models created using both training strategies exhibited a west-east geographic trend in the predictions for the favorability of hydrothermal resources. These models generally predicted higher favorability in western Nevada and lower favorability in eastern Nevada. This west-east trend in predicted favorability correlates with elevation across the Great Basin, which trends higher from west to east. By separating the original elevation feature into distinct features for elevation trend (i.e., regional-scale topography) and detrended elevation (i.e., valley-scale or local relative topography), we find that models using the separated topographic signals consistently outperform competing models that use the original elevation feature. Although western Nevada still exhibits higher favorability than eastern Nevada, using separated signals for regional elevation and local structure reduces the west-east prediction trend in the region and emphasizes structures associated with hydrothermal upflow. This work emphasizes how carefully engineering features to represent geological conditions relevant to hydrothermal systems allows ML algorithms to detect important patterns for predicting hydrothermal resource favorability and leads to better model performance.