Fifty megahertz band atmospheric radars (ARs) can detect clear air echoes and hydrometeor echoes simultaneously. However, in order to calculate spectral parameters (i.e., echo power, Doppler velocity, and spectrum width) of the clear air echo accurately, the clear air echo must be separated from the hydrometeor echo well. In this study, we propose methods (top method and two-echo method) for calculating the spectral parameters in precipitation region. The top method is used when raindrops or solid hydrometeors with small echo intensities exist. The top method sets an echo cut level by using the peak intensity of the clear air echo. The echo cut level is used for separating clear air echoes from hydrometeor echoes. The two-echo method is used when solid hydrometeors with large echo intensities exist. The two-echo method sets the echo cut level by using the local minimum of echo intensity between the clear air echo and the hydrometeor echo. Measurement results obtained by the vertical beam of the middle and upper atmosphere radar during a precipitation event on 26 October 2009 were used for evaluating the performance of the top and two-echo methods. The echo cut levels of the top and two-echo methods were determined from numerical simulation. The measurement results demonstrate that the top and two-echo methods are useful for reducing errors of spectral parameters.