The Advanced Topographic Laser Altimeter System (ATLAS) was launched aboard the Ice Cloud and land-Elevation Satellite-2 (ICESat-2) satellite in September 2018. ATLAS is a single wavelength (532 nm) lidar system designed to acquire high resolution measurements of the earth’s surface while also obtaining atmospheric backscatter from molecules, clouds, and aerosols. Because ATLAS is optimized for altimetry, the atmospheric data acquired is unique in many respects and requires non-standard analysis techniques. For example, the high repetition rate laser limits the vertical extent of the profiles to just 14 km and causes atmospheric scattering from above 15 km to be added to the scattering in the lower 0 -14 km profile. In addition, the limited vertical range of the acquired profiles renders it difficult to compute the magnitude of the solar background and hinders the application of standard calibration techniques. Despite these limitations, techniques have been developed to successfully produce data products that have value to the atmospheric community for cloud and aerosol research and are currently available at the National Snow and Ice Data Center (NSIDC). In this paper we describe the ICESat-2 atmospheric channel and the methods used to process the ATLAS raw photon count data to obtain calibrated backscatter and higher level products such as layer heights and type, blowing snow, column optical depth and apparent surface reflectance.