The integration of high-performance polymer substrates with added functionalities such as optical transparency and compatibility with micro-/nanolithography processes underpins future developments in flexible electronics and offers a myriad of applications such as displays, sensors, energy conversion etc. Recently, polyimide substrates such as Kapton® have emerged as an ideal choice for realizing high-performance, low-dimensional nanoelectronic platforms due to their high glass transition temperatures and chemical inertness. Flexible devices based on Kapton® polyimides, however, encounter fundamental challenges regarding the integration of optoelectronic platforms, due to their partly opaque optical characteristics. In this work, we realize a new photolithography process for wafer-scale patterning of metal microelectrode arrays (MEAs) on an optically transparent polyimide called Neopulim®. The newly established lithography protocol enabled the high throughput fabrication of flexible microchips with differently configured microelectrode arrays with uniform surface characteristics. The application potential of such optically transparent and flexible MEA chips is demonstrated by the realization of nanoscale devices based on two-dimensional graphene-based materials (GBMs) and one-dimensional zinc oxide nanowires (ZnO NWs). It is further shown that the use of Neopulim® with a high glass transition temperature (303 °C) characteristic withstands demanding device preparation steps such as use of thermal annealing and the self-assembly growth of NWs in a hot precursor solution, etc., opening a new chapter in the assembly and use of nanoscale optoelectronic platforms. The lithography procedure used to realize MEA chips and the fabrication of GBM and ZnO NW based optically transparent devices was characterized using state-of-the-art surface and electrical characterization tools. The devices were deployed as ion-sensitive field-effect transistors and as shown in this work, our devices provide an ideal platform for simultaneous optical and electrical readouts owing to high optical transparency. Scalable realization of optically transparent flexible devices at the nanoscale as presented in this work will open up new opportunities for next-generation platforms for optoelectronics, energy, sensors and biomedical applications.