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Advanced Encryption Standard algorithm was introduced to resist classical methods of cryptanalysis (i.e.) from linear or differential attacks. The cryptographic strength of the AES depends strongly on the choice of S-box. The result of the new attack methods shows that there may be some lacuna in the design of S-box in the AES algorithm. The setback is the weakness of the existing linearity structure in the S-box. After a detail analyze on the AES algorithm and a new performance scheme for rising complication of nonlinear transformation in the structure of S- box is presented in this paper. In order to resist from the new attacks and to execute the AES with the protected encryption and decryption by using JAVA and to provide a further more protection a Bio-metric scheme has been used in both the encryption and decryption schemes. The result shows that the new nonlinear implementation of the AES S-Box by using JAVA provides enhanced security with good enough speed for encryption and decryption.