Northern flying squirrels are part of a spotted owl-squirrel-fungi-tree connection that may be important to the long-term ecological health of forests within the Pacific Northwest.  After more than two decades of research, however, there is still conflicting information on important habitat components regulating squirrel populations.  Most previous studies contrast stand ages or management histories using two-dimensional data (e.g., live trapping), and suggest food as a primary limiting factor.  However, (1) flying squirrels occur in high abundances in forests that vary widely in age, management history, and food resources, (2) long-term radio-telemetry studies suggest that predation accounts for most regional squirrel mortality, and (3) squirrels use the entire three-dimensional space within a forest.  We therefore evaluated 33 forest stands across western Washington that varied in structural complexity to explore the hypothesis that three-dimensional structure is an important component of squirrel habitat, especially for providing protective cover as squirrels move outside their dens.  Data from live trapping studies, continuous-tracking of radio-collared squirrels, and vegetation surveys was collected from 1991-2006 and combined into an individual-based, spatially-explicit 3-D computer model.  Preliminary results suggest a positive association between high squirrel densities and forest structure created by interactions among tree density, multi-canopy layering, and canopy depth.  Removal of structure, either through natural or anthropogenic processes, appears to reduce squirrel densities.  Efforts to restore structural complexity across a dynamic, changing forest landscape may need to consider landscape permeability for organisms like flying squirrels and owls, especially before long-term benefits of ecology-based management activities are realized.