Electrogenic cells such as cardiomyocytes and neurons rely mainly on electrical signals for intercellular communication. Microelectrode array (MEA) devices have been developed to both record and stimulate electrogenic cell. This technology is fuels new insights in the operation of electrogenic cells and the operation of the brain, and is particularly suitable for long-term recording of cell signals under low cell stress conditions. To date, microelectrode arrays are relying on flat or needle shaped electrode surfaces, mainly due to limitations in the lithographic processes used to fabricate these electrodes. However, cells are intrinsically three-dimensional (3D), and this paper relies on a previously reported elasto-capillary aggregation process, to create 3D carbon nanotube (CNT) MEAs. We found that CNTs aggregated in well-shaped structures of similar size as cardiomyocytes are particularly interesting for MEA applications. This is because (i) CNT microwells of the right diameter preferentially trap individual cardiomyocytes , which facilitates single cell recording without the need for clamping pf cells or deconvolution of signals, and (ii) once the cells are trapped inside of the CNT wells, this 3D CNT structure is used as an electrode surrounding the cell, which increases the cell-electrode contact area and as a result we found that the recorded output voltages increase significantly(up to more than 200%). Further, our fabrication process allows for a large library of 3D geometries in a scalable fashion, which paves the way for future study of complex interactions between electrogenic cells and 3Drecording electrodes.