Border management and security challenges are increasing considerably in recent years. One of the major concerns is counterfeiting and fraudulent use of identity and other travel documents for crossing border controls. This poses serious threats and safety concerns worldwide, considering the scenario of terrorism and illegal migration across the world. Hence, advanced technologies with improved security features becomes essential to strengthen border security and to enable smooth transits. In this paper, we present a novel dual waveguide based invisible fluorescence security feature with lifetime discrimination and a simple validation system. Molecular fluorescence and lifetimes from the rare earth doped waveguides can be used as additional security features in the identity documents. The validation system consists of a modulated excitation source and fast photo-diodes which helps in the simultaneous detection of multiple security features from the fluorescence waveguides. The rare earth doped fluorescence waveguides are embedded into the identity document as micro-threads or tags which are invisible to the naked eye and are only machine readable. Rare earth fluorescence materials have higher sensitivity and selectivity as they absorb only specific ultraviolet (UV) or visible (VIS) wavelengths to create corresponding fluorescent emissions in the visible or infrared wavelengths. Herein, we present the results based on the fluorescence and fluorescence lifetime spectroscopic studies carried out on the terbium (Tb) and dysprosium (Dy) doped waveguides. The different emission wavelengths and lifetimes of these rare earth elements is a key differentiating feature, providing selectivity and security to the detector systems.