Among all the minutia based fingerprint identification system, the performance depends on the quality of input fingerprint images. In this paper, we have designed and implemented an algorithm of fingerprint image enhancement by using Iterative Fast Fourier Transform (IFFT). We have designed an approach for removing the false minutia generated during the fingerprint processing and a method to reduce the false minutia to increase the efficacy of identification system. We have used fingerprint Verification Competition 2006 (FVC 2006) as a database for implementation of proposed algorithm. Experimental results show that the results of our enhancement algorithm are better than existing algorithm of fast Fourier transform.