Successful implementation of climate change mitigation strategies requires a good understanding of the uncertainties of the strengths of greenhouse gas sources and sinks. The fossil fuel component of the global carbon budget is considered to be a very well constrained quantity; but recent studies suggest that the fossil fuel flux is not very well quantified in scales finer than the US state level. Thus, there is a critical need for accurate measurements and inventories, as well as to develop approaches to evaluate the uncertainties of these measurements. The Indianapolis flux experiment aims to address our knowledge gap through the development and evaluation of measurement strategies to better constrain uncertainties in urban greenhouse gas emission using Indianapolis as a case study. We present results from several aircraft-based measurements in Indianapolis. Citywide emissions of greenhouse gases (CO2 and CH4) were quantified using a combination of cavity ring-down spectroscopy, flask measurements and a mass balance approach on an aircraft-based platform. We investigate the sensitivity of the estimated emissions to changes in various measurement and model parameters, e.g., regional background concentration of CO2 and CH4, height of the convective boundary layer, wind speed and direction, and choice of interpolation techniques used in the mass balance calculations. The results of this study will help us gain a better grasp of the accuracy of aircraft-based measurements of urban fossil fuel emissions.