Ultrathin Silk-Based Brain Implants
hatboyzero writes "University of Pennsylvania engineers have designed silk-based electronics that can stick to the surface of the brain, allowing for better brain-computer interfaces. The researchers say the silk-based devices are thin and flexible enough to reach previously inaccessible areas of the brain."
http://xkcd.com/644/
Quite a bit is localized to the cortex, such as motor control. It's also used for higher thought, but that's too random to really do much with. Humans have the most advanced cortex of any animal, although that also means it's thicker (1.5 - 4.5 mm), which may present the problem you propose.
The brains cortex is where all the processing is done. When we go deeper into the brain what you get are long axons that interconnect regions of the brain. In the middle of the brain is the corpus collosum which acts an information transfer center from the left to the right brain and vice versa. Now the cortex its self is a 3 dimensional matrix, as you said. I doubt we will be able to (in any near future scenario) build small enough electrodes and exact placement techniques as to make brain implants that function perfectly along side our own brain activity. This silk interface is good for rough signaling and signal reception... which is a great first step. /tangent
Eat sleep die
Schreibman Port
Just saying.