Yellow pine and mixed-conifer (YPMC) forests of California’s Sierra Nevada have experienced widespread fire suppression for over a century, resulting in ingrowth and densification of trees, heavy fuel accumulation, and shifts in species composition. Under warmer and drier climates, these forests are primed for stand-replacing fires and severe drought mortality, requiring management interventions to improve their resilience and mitigate future impacts. Observations from functioning frequent-fire systems (e.g., contemporary reference sites) can provide key insights about pattern-process relationships in fire-intact systems, which can be used to inform regional management efforts. In this study, we used airborne lidar data to quantify and compare forest structure at multiple spatial scales between contemporary reference sites (i.e., forests with a restored frequent, low-intensity fire regime) and control sites (i.e., typical fire-suppressed forests). We evaluated structures at the neighborhood- (∼1 ha), site- (∼100–1,000 ha), and among-site- (∼10,000–100,000 ha) levels. In reference sites, high proportions of individual trees, small clumps of 2–4 trees, and open space formed mostly open canopy structures at the neighborhood-level, and patches of these neighborhood-level structures were arranged in heterogeneous spatial patterns within sites. We observed low variability in site-level structures among reference sites, indicating a stabilizing effect of frequent, low-intensity fire across broad, ecosystem scales. In fire-suppressed control sites, edaphic factors and other non-fire disturbances occasionally produced heterogeneity at the neighborhood- and site-level, but the degree of heterogeneity was not consistent across sites. Structural patterns in contemporary reference sites suggest improved resilience to future disturbances and climate change, and increased provisioning of ecosystem services relative to control sites. We suggest applying these metrics to help inform multi-scale and multi-resource management in Sierra Nevada forests.