Herein we report a new transparent nanostructured Fabry-Perot interferometer (FPI) device. The unique features of the nanostructured optical device can be summarized as the following: (i) optically transparent nanostructured optical device; (ii) simple and inexpensive for fabrication; (iii) easy to be fabricated and scaled up as an arrayed format. These features overcome the existing barriers for the current nanopore-based interferometric optical biosensors by measuring the transmitted optical signals rather than the reflected optical signals, thereby facilitating the optical testing significantly for the arrayed biosensors and thus paving the way for their potential for high throughput biodetection applications. The optically transparent nanostructures (i.e., anodic aluminum oxide nanopores) inside the FPI devices are fabricated from 2.2 microm thick lithographically patterned Al thin film on an indium tin oxide (ITO) glass substrate using a two-step anodization process. Utilizing the binding between Protein A and porcine immunoglobulin G (IgG) as a model, the detection of the bioreaction between biomolecules has been demonstrated successfully. Experiments found that the lowest detection concentration of proteins is in the range of picomolar level using current devices, which can be easily tuned into the range of femtomolar level by optimizing the performance of devices.