Processing data from high-altitude, airborne lidar instruments that employ single-photon sensitive, arrayed detectors poses several challenges. Arrayed detectors produce large volumes of data; single-photon sensitive detectors produce high levels of noise; and high-altitude operation makes accurate geolocation difficult to achieve. To address these challenges, a unique and highly automated processing chain for high-altitude, single-photon, airborne lidar mapping instruments has been developed. The processing chain includes algorithms for coincidence processing, noise reduction, self-calibration, data registration, and geolocation accuracy enhancement. Common to all single-photon sensitive systems is a high level of background photon noise. A key step in the processing chain is a fast and accurate algorithm for density estimation, which is used to separate the lidar signal from the background photon noise, permitting the use of a wide-range gate and daytime operation. Additional filtering algorithms are used to remove or reduce other sources of system and detector noise. An optimization algorithm that leverages the conical scan pattern of the instrument is used to improve geolocation and to self-calibrate the system.