A nanopore FET sensor device and method of making. The nanopore FET sensor device includes a FET device stack of material layers including a source, channel and drain layers, and a nanoscale hole through the FET device stack to permit flow of strands of molecular material, e.g., DNA, therethrough. The perimeter of the nanoscale hole forms a FET device gate surface. The source and drain layers are provided with respective contacts for connection with measuring instruments that measure a flow of current therebetween. The molecular strands having charged portions pass from one side of a wafer substrate to the other side through the (nanopore) gate and modulate the current flow sensed at the source or drain terminals. The sensor collects real-time measurements of the current flow modulations for use in identifying the type of molecule. Multiple measurements by the same nanopore FET sensor are collected and compared for enhanced detection.