Using neural probing devices implanted in the brain, neural activity from neural cells can be recorded in-vivo for long term periods. This research goal is to develop and investigate a neural sensing device using nanotechnology which can enhance the quality and longevity of sensing. In this research, two neural electrode designs were employed with nanostructures, which distinguish them from 2-dimensional planar electrode configuration. According to electrochemical simulation, high molecular confinement has been observed on vertically aligned nanowire electrodes, especially those with grid structures. The efficacy of the 3-dimensional nanoelectrode is also discussed in this paper, depending on the molecular diffusion on nanoelectrodes.© (2011) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.