A 1.29 GHz wind profiler was developed under a private–military–government cooperative wind profiler radar development project in the Republic of Korea. During the test operation period, radio frequency interference (RFI) contamination occurred in the spectrum. In addition to the general shape, with a continuous appearance depending on the altitude, the spectrum showed complex shapes, such as discontinuous and overlapping frequencies. The RFI characteristics in the wind profiler spectra were analyzed, and a new algorithm was developed to remove multiple RFI (MRFI). Meteorological and non-meteorological signals were separated by filtering with a spectrum width threshold of 0.1 m/s. A continuity check was performed to determine MRFI in the non-meteorological signal. The number of gates in which the same radial velocity is continuous was determined based on whether the beam was vertical or oblique; a rough continuity test was performed, considering exceptional circumstances for the meteorological signal. For overlapping MRFI, the process was repeated. Spectral contamination by MRFI was removed through filtering and iterated scans; the continuity of wind vectors calculated from the improved spectral radial velocity was verified. Good-quality wind vectors can be produced even in a bad-radio-frequency environment if proper quality control is performed.