In this study, we developed microfabricated porous membranes aimed at facilitating innervation in 3D cell culture models. The aim of the paper is to introduce a fabrication method for porous membranes with adjustable size, shape and location of the pores without obstructing imaging or the connectivity of the cells. The method is based on making a patterned SU-8 layer on a sacrificial aluminium layer by UV lithography and releasing it with etching. With the proposed method, we were able to produce single-layer self-supporting membranes that were used as interfaces in compartmentalized microfluidic devices. The functionality of the membranes and their cytocompatibility were tested by culturing human pluripotent stem cell (hPSC)-derived neurons on their surfaces. In vitro experiments demonstrated that a dense neural network develops on top of the proposed membranes within a week. Neurites were able to migrate through the pores to the bottom side of the membranes. We achieved partial, but still significant, axonal isolation. The results of this study will pave the way for the development of optimized innervated tissue models by using the combination of porous SU-8 membrane substrates, microelectrode arrays and hPSC-derived neurons in compartmentalized cell cultivation devices.