Abstract. There is a widely recognized need to improve our understanding of biosphere-atmosphere carbon exchanges in areas of complex terrain including the United States Mountain West. CO₂ fluxes over mountainous terrain are often difficult to measure due to unusual and complicated influences associated with atmospheric transport. Consequently, deriving regional fluxes in mountain regions with carbon cycle inversion of atmospheric CO₂ mole fraction is sensitive to filtering of observations to those that can be represented at the transport model resolution. Using five years of CO₂ mole fraction observations from the Regional Atmospheric Continuous CO₂ Network in the Rocky Mountains (Rocky RACCOON), five statistical filters are used to investigate a range of approaches for identifying regionally representative CO₂ mole fractions. Test results from three filters indicate that subsets based on short-term variance and local CO₂ gradients across tower inlet heights retain nine-tenths of the total observations and are able to define representative diel variability and seasonal cycles even for difficult-to-model sites where the influence of local fluxes is much larger than regional mole fraction variations. Test results from two other filters that consider measurements from previous and following days using spline fitting or sliding windows are overly selective. Case study examples showed that these windowing-filters rejected measurements representing synoptic changes in CO₂, which suggests that they are not well suited to filtering continental CO₂ measurements. We present a novel CO₂ lapse rate filter that uses CO₂ differences between levels in the model atmosphere to select subsets of site measurements that are representative on model scales. Our new filtering techniques provide guidance for novel approaches to assimilating mountain-top CO₂ mole fractions in carbon cycle inverse models.