In recent years, microfluidic systems have evolved to incorporate increasingly complex multi-layer and multi-material structures. While conventional 2-dimensional microfluidic systems are typically fabricated with lithographic techniques, the increase in system complexity necessitates a more versatile set of fabrication techniques. Similarly, although 3D printing can easily produce intricate microfluidic geometries, integrating multiple membranes and electrode components remains challenging. This study proposes a toolkit for fabricating free-standing 3-dimensional microfluidic systems for biomedical devices, incorporating flow channels, electrodes, and membranes. The fabrication techniques include molding separation using 3D printed molds, laser-based processing, and component assembly, each achieving micron resolution. Here, we introduce a novel approach to integrate membranes into microfluidics by directly curing elastomer-based microfluidics with the membrane through replica molding, while preserving membrane functionality by effectively removing elastomer residues through reactive ion etching. The resulting membrane-elastomer microfluidic component significantly simplifies the assembly of intricate microfluidic systems, reducing the device size to millimeter dimensions, suitable for implantable applications. The toolkit's versatility is demonstrated by a redox flow iontophoretic drug delivery prototype at the millimeter scale, featuring two electrodes, four membranes, and four microfluidic channels.