In order to provide the high sensitivity SERS active substrates needed for rapid and sensitive chemical/biological agent detection, the present invention provides a Plasmonic Nano-antenna Array (PNA) substrate with large local electromagnetic field enhancements; a controllable and repeatable nano-fabrication process for creating the PNA surface; and a system design for a compact, portable device capable of using the PNA technology to acquire and analyze target molecular samples. Both 2D and 3D systems are provided.