Embodiments relate to providing security of scan mode access and data in an integrated circuit. In embodiments, one or both of two layers of security are provided. A first layer includes requiring a complex initialization sequence to be performed in order to access scan mode. A second layer includes scrambling the scan data before it is output from the circuit under test, which prevents unauthorized persons from extracting useful information from the output scan data. Further embodiments relate to methodologies for utilizing these protection layers after manufacture of the integrated circuit and incorporating these protection layers in an integrated circuit design flow.