We describe the challenges associated with the interpretation of extinction coefficient measurements by the Stratospheric Aerosol and Gas Experiment (SAGE II) in the presence of clouds. In particular, we have found that tropospheric aerosol analyses are highly dependent on a robust method for identifying when clouds affect the measured extinction coefficient. Herein, we describe an improved cloud identification method that appears to capture cloud/aerosol events more effectively than early methods. In addition, we summarize additional challenges to observing the Asian Tropopause Aerosol Layer (ATAL) using SAGE II observations. Using this new approach, we perform analyses of the upper troposphere, focusing on periods in which the UTLS (upper troposphere/lower stratosphere) is relatively free of volcanic material (1989–1990 and after 1996). Of particular interest is the Asian monsoon anticyclone where CALIPSO (Cloud-Aerosol Lidar Pathfinder Satellite Observations) has observed an aerosol enhancement. This enhancement, called the ATAL, has a similar morphology to observed enhancements in long-lived trace gas species like CO. Since the CALIPSO record begins in 2006, the question of how long this aerosol feature has been present requires a new look at the long-lived SAGE II data sets despite significant hurdles to its use in the subtropical upper troposphere. We find that there is no evidence of ATAL in the SAGE II data prior to 1998. After 1998, it is clear that aerosol in the upper troposphere in the ATAL region is substantially enhanced relative to the period before that time. In addition, the data generally supports the presence of the ATAL beginning in 1999 and continuing through the end of the mission, though some years (e.g., 2003) are complicated by the presence of episodic enhancements most likely of volcanic origin.