We recommend an automated statistical method (Moving Point Test, or MPT) to determine the friction velocity (u*) thresholds in nighttime eddy flux filtering. Our intention is to make the determination of the u* thresholds objective and reproducible and to keep flux treatment consistent over time and across sites. In developing the MPT method, we recognize that both ecosystem respiration and u* exhibit diurnal and seasonal cycles and there are potential correlative changes between them, which must be removed before u*can be used as a filter criterion. MPT uses an iterative approach to simultaneously determine a valid temperature response function, which is used to normalize nighttime flux measurements, and identify u* thresholds based on the normalized fluxes. Tests show that MPT works well for a variety of scenarios and vegetation types. We also recommend that in order to increase the reliability of nighttime flux filters, a detailed measurement of mean CO2 concentration profiles need to be employed to calculate canopy storage changes accurately. Preferably, multiple profiles at different locations within the nighttime flux footprint should be used so that volume-averaged storage changes can be made. In addition, efforts should be made to minimize measurement gaps in summer nights as much as possible because of the short-time duration and frequent calm conditions, which greatly limit the amount of reliable data. We emphasize that the MPT method is not meant to be a final solution to the nighttime flux issue. Continuous theoretical and experimental researches are still needed to overcome the challenges in measuring nighttime fluxes accurately.