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Biometrics is beginning to gain wide spread acceptance as the future of authentication and authorization. Like other systems, biometric based security systems have vulnerabilities that attackers can exploit to gain unauthorized access. To our knowledge there is no standard model to fully understand and standardize the design of the secure biometric systems. This paper proposes a functional model that represents biometric systems. This model can be used as a solid ground for studying, designing, and implementing secure biometric systems. To clarify the benefits of the proposed model, the paper discusses the biometric system components in light of the model. Also, the paper discusses various vulnerabilities of the biometric system from view of the functional model. Finally, the paper evaluates some countermeasures of these vulnerabilities and proposes novel solutions to some of them.