Decisions regarding the level of detail included in conservation planning and the importance given to feasibility considerations can greatly influence management in terms of total area required, achievement of conservation targets and costs. This work had two main objectives: (1) to compare priority sites proposed by the Chilean commission for the environment in a politically driven process to the results of alternative systematic conservation planning scenarios; and (2) to compare the efficacy of systematic conservation planning based on different types of conservation targets (forest types and bird species) and minimum area thresholds. To address these issues, we used vegetation cover as well as field data on forest birds in central Chile. Bird species distributions were modeled using a variety of climatic and environmental layers, allowing for the integration of environmental heterogeneity into the planning process. We then ran several conservation planning scenarios considering conservation targets based on vegetation types alone, birds alone, or a combination of vegetation and birds. Collectively these results show that conservation planning results differ significantly when considering birds or vegetation types, and that minimum area requirements for each conservation feature has a great influence on the final results. Moreover, important conservation sites are not represented in the current government plan, and these sites are related to the small representation of rare vegetation types. This study suggests that using appropriate minimum area requirements can greatly affect the results of a conservation planning exercise and therefore represents a key knowledge gap in the region.