Studies of electrically induced morphological changes in neurons have either been limited by the resolution of light microscopy or the cell fixation required for electron microscopy. Atomic force microscopy (AFM), however, mechanically maps cell topography, offering exquisite resolution of evolving processes in three dimensions. In this paper, we present a microelectrode array (MEA) based platform for the real-time detection of subtle, electrically induced variations in neuronal morphology, with AFM. This platform required the customized design and production of a silicon-based MEA, integration with a commercial AFM, and the development of biological techniques for culture of neuroblastoma (SH-SY5Y) cells onto the device. Biphasic pulse trains (1 Hz) of electric current were delivered to a microelectrode interfaced with a neuroblastoma cell, and the AFM continuously recorded a cross-sectional height profile. Proof-of-principle experiments demonstrate that electric stimulation may induce fluctuations ranging in the 100-300-nm range, 75-fold greater than the systemic resolution, but smaller than the resolution of light microscopy modalities. In addition, the real-time capabilities of AFM captured a collapse (30%-40%) of a neurite cross section, seconds after electric stimulation. Ultimately, this platform can be used to nanocharacterize cell responses to electric stimulation and other biochemical cues, for use in neuronal patterning and regeneration studies.