Implantable active electronic microchips are being developed as multinode in-body sensors and actuators. There is a need to develop high throughput microfabrication techniques applicable to complementary metal–oxide–semiconductor (CMOS)-based silicon electronics in order to process bare dies from a foundry to physiologically compatible implant ensembles. Post-processing of a miniature CMOS chip by usual methods is challenging as the typically sub-mm size small dies are hard to handle and not readily compatible with the standard microfabrication, e.g., photolithography. Here, we present a soft material-based, low chemical and mechanical stress, scalable microchip post-CMOS processing method that enables photolithography and electron-beam deposition on hundreds of micrometers scale dies. The technique builds on the use of a polydimethylsiloxane (PDMS) carrier substrate, in which the CMOS chips were embedded and precisely aligned, thereby enabling batch post-processing without complication from additional micromachining or chip treatments. We have demonstrated our technique with 650 μm × 650 μm and 280 μm × 280 μm chips, designed for electrophysiological neural recording and microstimulation implants by monolithic integration of patterned gold and PEDOT:PSS electrodes on the chips and assessed their electrical properties. The functionality of the post-processed chips was verified in saline, and ex vivo experiments using wireless power and data link, to demonstrate the recording and stimulation performance of the microscale electrode interfaces.