Various methods of manufacture can produce three-dimensional, high density, high-electrode probe arrays that can advantageously be used in neural-based applications. In one example, deep reactive ion etched (DRIE) ultra-high aspect ratio holes are etched in silicon and refilled with multiple films to a high density array of individual probes, each probe having individual recording and/or stimulation sites or tips. Using a DRIE lag effect technique can help control tip sharpness and electrode length, allowing for narrow, long, and dense needles to be formed side-by-side in a single array. In some examples, multimodal probe arrays are manufactured, with some probes having a recording/stimulating site, other probes having a waveguide, and yet other probes having a microfluidic channel.