Increasing the proximity of microelectrode arrays (MEA) to targeted neural tissues can establish efficient neural interfaces for both recording and stimulation applications. This has been achieved by constructing protruding three-dimensional (3D) structures on top of conventional planar microelectrodes via additional micromachining steps. However, this approach adds fabrication complexities and limits the 3D structures to certain shapes. We propose a one-step fabrication of MEAs with versatile microscopic 3D structures via “microelectrothermoforming (μETF)” of thermoplastics, by utilizing 3D-printed molds to locally deform planar MEAs into protruding and recessing shapes. Electromechanical optimization enabled a 3D MEA with 80 μm protrusions and/or recession for 100 μm diameter. Its simple and versatile shaping capabilities are demonstrated by diverse 3D structures on a single MEA. The benefits of 3D MEA are evaluated in retinal stimulation through numerical simulations and ex vivo experiments, confirming a threshold lowered by 1.7 times and spatial resolution enhanced by 2.2 times.