Cell culture systems have validated to be able to mimic living organisms for various biological applications. In the current study, we demonstrated a method of fabricating three-dimensional (3D) cell culture system by stacking multiple layers of polydimethylsiloxane (PDMS) embedded with functionalized hydroxypropyl cellulose methacrylate (HPC-MA) porous scaffolds, which were connected through thread as a readymade hydrophilic channel. Thread could wick and distribute micro volumes of liquid samples from single inlet point into arrays of detection and working zones without the requirement of either pump or external pressure. Thread with an average thickness of 300μm provided sufficient rate to continuously supply the media into the system in less than 250s and remove waste from the cell culture system. The number of COS-7 cells present in the multilayer culture system was comparatively identical to the cells grown in the tissue culture dish and scaffold in a microwell plate. This multilayer cell culture system can be applied to implantable biodegradable poly(lactic-co-glycolic acid) (PLGA) suture as well as initiating cell differentiation in multilayers.