3D printing and makerspace technologies are increasingly explored as alternative techniques to soft lithography for making microfluidic devices, and for their potential to segue towards scalable commercial fabrication. Here we considered the optimal application of current benchtop 3D printing for microfluidic device fabrication through the lens of lean manufacturing and present a straightforward but robust rapid prototyped moulding system that enables easy estimation of more precise quantities of polydimethylsiloxane (PDMS) required per device to reduce waste and importantly, making devices with better defined depths and volumes for (i) modelling gas exchange and (ii) fabrication consistency as required for quality-controlled production. We demonstrate that this low-cost moulding step can enable a 40 – 300% reduction in the amount of PDMS required for making individual devices compared to the established method of curing approximately 30 grams of PDMS prepolymer overlaid on a 4” silicon wafer master in a standard plastic petri dish. Other process optimisation techniques were also investigated and are recommended as readily implementable changes to current laboratory and foundry-level microfluidic device fabrication protocols for making devices either out of PDMS or other elastomers. Simple calculators are provided as a step towards more streamlined, software controlled and automated design-to-fabrication workflows for both custom and scalable lean manufacturing of microfluidic devices.