We propose a new method to apply shape analysis techniques to a computational auditory scene analysis (CASA)-based speech separation system. The conventional CASA-based speech separation system extracts speech signals from a mixture of speech and noise signals. In the proposed method, we complement the missing speech signals by applying the shape analysis techniques such as labelling and distance function. In the speech separation experiment, the proposed method improves signal-to-noise ratio by 6.6 dB. When the proposed method is used as a front-end of speech recognizers, it improves recognition accuracy by 22% for the speech-shaped stationary noise condition and 7.2% for the two-talker noise condition at the target-to-masker ratio than or equal to -3 dB.