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Abstract: Quantifying trace gas emissions and the influence of surface exchange processes on the atmosphere is a necessary step towards the control of global greenhouse gas emissions and reliability of air quality models. This paper proposes a procedure based on the mass balance method and implemented on highly resolved aircraft data. It allows one to estimate surface exchanges on areas of several km2 and heterogeneous features exploiting the characteristics of convective boundary layer during steady state conditions that permit the estimation of emission/absorption terms as functions of advective fluxes only. A nonparametric approach is adopted and the fluxes on the surface of a virtual box surrounding the area of interest are reconstructed on the basis of scalar densities and wind vectors using Shepard functions. Two different techniques are also proposed to face lack of data on the top surface of the box. The method has been applied to experimental data coming from measurement campaigns on two different sites. It provides realistic estimates of the CO2 emission/absorption in the considered areas that are in good agreement with CO2 fluxes evaluated by Airborne Eddy Covariance and confirm the suitability of the proposed approach for the assessment of turbulent exchange of trace gases by composite landscapes. Uncertainties on the estimated emissions due to both propagation of the experimental error and interpolation have been quantified by bootstrap analysis as 6%. [Copyright &y& Elsevier]