This paper has developed a modal identification method for ringdown frequency data of low SNR and LFO deformation. Noise effect on modal identification was reduced by using a Prony-based method with threshold for truncation of SVs in SVD. An effectual modal impulse response was determined by omitting a deformed portion from a difference sequence of two sets of ringdown frequency data. The feasibility of the developed method was shown to identify the EI and the WECC systems from FNET ringdown frequency data.