Prey species use structures such as burrows to minimize predation risk. The spatial arrangement of these resources can have important implications for individual and population fitness. For example, there is evidence that clustered resources can benefit individuals by reducing predation risk and increasing foraging opportunity concurrently, which leads to higher population density. However, the scale of clustering that is important in these processes has been ignored during theoretical and empirical development of resource models. Ecological understanding of refuge exploitation by prey can be improved by spatial analysis of refuge use and availability that incorporates the effect of scale. We measured the spatial distribution of pygmy rabbit (Brachylagus idahoensis) refugia (burrows) through censuses in four 6-ha sites. Point pattern analyses were used to evaluate burrow selection by comparing the spatial distribution of used and available burrows. The presence of food resources and additional overstory cover resources was further examined using logistic regression. Burrows were spatially clustered at scales up to approximately 25 m, and then regularly spaced at distances beyond ~40 m. Pygmy rabbit exploitation of burrows did not match availability. Burrows used by pygmy rabbits were likely to be located in areas with high overall burrow density (resource clusters) and high overstory cover, which together minimized predation risk. However, in some cases we observed an interaction between either overstory cover (safety) or understory cover (forage) and burrow density. The interactions show that pygmy rabbits will use burrows in areas with low relative burrow density (high relative predation risk) if understory food resources are high. This points to a potential trade-off whereby rabbits must sacrifice some safety afforded by additional nearby burrows to obtain ample forage resources. Observed patterns of clustered burrows and non-random burrow use improve understanding of the importance of spatial distribution of refugia for burrowing herbivores. The analyses used allowed for the estimation of the spatial scale where subtle trade-offs between predation avoidance and foraging opportunity are likely to occur in a natural system.