Abstract We present a method to mitigate the atmospheric effects (residual atmospheric lines) in single-dish radio spectroscopy caused by the elevation difference between the target and reference positions. The method is developed as a script using the Atmospheric Transmission at Microwaves (ATM) library built into the Common Astronomy Software Applications (CASA) package. We apply the method to the data taken with the Total Power Array of the Atacama Large Millimeter/submillimeter Array. The intensities of the residual atmospheric (mostly O₃) lines are suppressed by, typically, an order of magnitude for the tested cases. The parameters for the ATM model can be optimized to minimize the residual line and, for a specific O₃ line at 231.28 GHz, a seasonal dependence of a best-fitting model parameter is demonstrated. The method will be provided as a task within the CASA package in the near future. The atmospheric removal method we developed can be used by any radio/millimeter/submillimeter observatory to improve the quality of its spectroscopic measurements.