During the ACRIDICON-CHUVA aircraft campaign in September 2014 over the Amazon, among other topics aerosol effects on the development of cloud microphysical profiles during the burning season were studied. Hyperspectral remote sensing with the imaging spectrometer specMACS provided cloud microphysical information for sun-illuminated cloud sides. In order to derive profiles of phase or effective radius from cloud side observations vertical location information is indispensable. For this purpose, spectral measurements of cloud side reflected radiation in the oxygen-A absorption band collected by specMACS were used to determine absorption path length between cloud sides and the instrument aboard the aircraft. From these data horizontal distance and eventually vertical height were derived. It is shown that, depending on aircraft altitude and sensor viewing direction, an unambiguous relationship of absorption and distance exists and can be used to retrieve cloud geometrical parameters. A comparison to distance and height information from stereo image analysis (using data of an independent camera) demonstrates the efficiency of the approach. Uncertainty estimates due to method, instrument and environmental factors are provided by the method. Main sources of uncertainty are unknown in-cloud absorption path contributions due to complex 3D geometry or unknown microphysical properties, variable surface albedo and aerosol distribution. A systematic difference of 3.8 km between stereo and spectral method is found which can be attributed to 3D geometry effects not considered in the methods simplified cloud model. If this offset is considered, typical differences found are 1.6 km for distance and 230 m for vertical position at a tpyical distance around 20 km between sensor and convective cloud elements of typically 1–10 km horizontal and vertical extent.