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Cognitive radio is a revolutionary evolution of future wireless communication to utilize the unused part of the spectrum, which is actually assigned to licensed services only. An NC_OFDM based cognitive radio has the capability to nullify individual sub carriers to avoid interference with the licensed user. So, that there could be a large number of zero valued inputs/outputs compare to non-zero terms. From the standard structure of OFDM we can find that IFFT/FFT modules play the vital role for any OFDM based transceiver. So when zero valued inputs/outputs outnumber nonzero inputs/outputs, then general IFFT/FFT algorithm for OFDM is no longer efficient in term of execution time. It is possible to reduce the execution time by “pruning” the FFT. In this paper we have implemented a novel and efficient input zero traced FFT pruning (IZTFFTP) algorithm based on DIF radix-2 technique. Compare to other algorithms, the results of IZFFTP shows that it is independent of the position of the zero valued input and also maintaining a good trade-off between time and space complexity of any system by not only reducing the number of complex multiplication as well as complex additions also extraordinarily. The proposed algorithm is implemented in high level computer program i.e. in C++ and this is similar to the Cooley-Tukey radix-2 FFT algorithm, retaining all the key features such as simplicity and regularity, by making some alternation and programming modification.