Cortical modularity and nanotechnology might look like a strange pair of concepts taken together, but nevertheless they seem very much suited for each other. Indeed, cortical modularity is a fundamental microanatomic feature of the brain while nanotechnology with its nanometric precision provides nanoscale structures, namely nanowires and carbon nanotubes capable of interacting with the brain at the genetic, molecular, and microcircuit level. Research in neuroscience is essentially a combination of many interdisciplinary sciences where nanoscience and nanotechnology plays a pivotal role. In this chapter we examine carbon nanotubes (CNTs) and nanowires (NWs), and their potential to uncover the function of cortical microcircuits, as well as novel applications for diagnosis and treatment of brain diseases. For example, the simultaneous recording from cortical minicolumns with multi-electrode arrays (MEAs) consisting of CNTs or NWs is emerging for developing cognitive prostheses for a broad range of neurological and psychiatric dysfunctions.