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The quality of cleft lip and palate (CLP) speech is affected due to hyper-nasality and mis-articulation. Surgery and speech therapy are required to correct the structural and functional defects of CLP, which will result in an enhanced speech signal. The quality of the enhanced speech is perceptually evaluated by speech-language pathologists and results are highly biased. In this work, a signal processing based two stage speech enhancement method is proposed to get the perceptual benchmark to compare the signal after the surgery / therapy. In the first stage, CLP speech is enhanced by suppressing the nasal formant and in the second stage, spectral peak-valley enhancement is carried out to reduce the hyper-nasality associated with the CLP speech. The evaluation results show that the perceptual quality of CLP speech signal is improved after enhancement in both stages. Further, the improvement in the quality of the enhanced signal is compared with the speech signal after palatal prosthesis / surgery. The perceptual evaluation results show that the enhanced speech signals are better than the speech after prosthesis / surgery