This paper presents a manufacturing process for flexible optical waveguides made of biocompatible polydimethylsiloxane (PDMS) to be attached to future optogenetic implants. Based on a complementary metal-oxide-semiconductor (CMOS) application-specific integrated circuit (ASIC), the system uses integrated single photon avalanche diodes (SPADs) as sensors for fluorescence imaging (FI) and post-CMOS micro light-emitting diodes (µLEDs) for stimulation [1]. Attaching fibers to SPADs and µLEDs to collect and distribute light from and to deeper brain layers can unfold previously unachieved medical applications. Two technologies for biocompatible waveguide manufacturing are presented: thin-film and molding. Such a combination of integrated bidirectional implantable ASICs with custom waveguide manufacturing is not limited to medical scenarios but opens up a broad field of applications.