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In this paper, we have presented a new fast Fourier transform representation based cryptographic (encryption) system for the multimedia data security. The key features of the proposed system are: 1. Mapping/representation of the fast Fourier transforms' structure based on discrete orthogonal transforms, such as Walsh-Hadamard, Haar, and complex Walsh-Hadamard, etc. 2. The efficient implementations of the encryption within the core of the fast Fourier transform (flexibility in the shuffling of the sensitive information). In addition to these key features, the computational complexity of the system is comparable with commonly used methods. One of the important differences between the existing transform based encryption systems, and the proposed is that the encryption has been done in the core of the transform, which ultimately provides the highest level of security to the sensitive data. The proposed system consequently has the dual key security feature, which consists of the encryption and the transform dependent keys.