A MBES (multibeam echo sounder) survey around Yokji Island, Korea, was conducted to find an effective method for removing error data. Two post-processing software programs, PDS2000 (RESON) and HIPS (CARIS), were used to remove the error data using an interactive editing method and the CUBE algorithm filter. The post-processing with the PDS2000 and HIPS programs, using the interactive editing method, took 120 and 168 hours, respectively, and there was little difference in the seafloor images. The processing time of the PDS2000 and HIPS programs using the CUBE algorithm filter was 36 and 60 hours, respectively. Nevertheless, there was little difference in the seafloor images because of differences in the factor parameters in each of the post-processing programs. Therefore, post-processing using CUBE filtering can save time in data processing and provide consistent results, excluding the subjective decisions of the operator. This method is more effective than other methods for rejecting erroneous multibeam echo sounder data.