3D photonic integration introduces a new degree of freedom in the design of photonic integrated circuits (PICs) compared to standard 2D-like structures. Novel applications such as large-scale optical switching matrices, e.g. for top-of- rack cross connect switches in data centers, benefit from the additional design flexibility due to their waveguide crossing-free architecture and compact footprint. In this work, a novel 3D 4×4 multi-mode interference coupler (MMI) based on HHI’s polymer-based photonic integration platform PolyBoard is presented. The fabrication process of the PolyBoard platform allows for the realization of vertically stacked polymer waveguide layers. Cascading two of the presented 3D 4×4 MMIs will form the building block of future large-scale 3D switching matrices. The 3D 4×4 MMI structure comprises two waveguide layers separated by a distance of 7.2 μm, with two input and two output waveguides in each layer, and a multimode interference (MMI) section in between. The vertical MMI section serves as the interconnection between the different waveguide layers and distributes the incoming light from each input waveguide across the four output ports of the 4×4 MMI. Design rules and fabrication methodology of these novel structures are presented in detail. Preliminary measurements demonstrate the proof-of-concept indicating an insertion loss below 9.3 dB, including fiber-chip coupling loss and the 6 dB intrinsic loss.