The Jicamarca incoherent scatter radar can be operated in different modes to measure the main physical parameters of the equatorial ionosphere. One of these modes is the Faraday/Double Pulse experiment that was designed to estimate F -region plasma densities and electron/ion temperatures by pointing the Jicamarca antenna beam off-perpendicular to the geomagnetic field. For several years, the data processing for this mode was performed in time domain (correlation analysis), but sometimes the data is contaminated with frequency interference and other unwanted signals that are not easy to remove. To obtain better results, a spectral analysis procedure for this mode has been implemented in Signal Chain, a python-based radar signal processing library developed at the Jicamarca Radio Observatory. Signal Chain includes algorithms for interference and clutter removal to clean the spectral data before estimating the geophysical parameters. The procedure applies an outlier removal algorithm before calculating incoherently averaged power spectra. This algorithm, based on the Hildebrand-Sekhon method, is applied to sequences of spectral data for each frequency bin. Then, the DC clutter from the self- and cross-spectra is removed as a second step in the cleaning process. In this work, we present the results obtained with the spectral analysis procedure applied to the the FaradaylDouble Pulse experiment and compared the electron densities estimated with this method with the ones obtained with the standard correlation analysis.