The key hurdle in nanoscience and nanotechnology is the large-scale integration of nanoscale materials with micron scale electronics and structures to form functional devices and sensors. We have developed an innovative bottom-up wafer scale fabrication method that combines nanopatterning and nanomaterials synthesis with traditional silicon micromachining technologies. We have achieved nano-micro integration through catalyst nanopatterning and registration at wafer scale and through effective nanocatalyst protection and release before and after microfabrication. Our wafer scale fabrication process has produced 244 carbon nanotube (CNT) probes per 4-inch silicon wafer with control over the CNT location, diameter, length, orientation, and crystalline morphology. CNT probes with diameters of 40-80 nm and lengths of 2-6 μm are found to be functional nano probes for atomic force microscopy (AFM) imaging. In this paper, we will address our nano probe design and fabrication considerations in detail. CNT tip locations and diameters are defined by e-beam lithography. CNT length, orientation, and crystalline quality are controlled by the plasma enhanced chemical vapor deposition (PECVD) method. With effective catalyst protection schemes, this fabrication process is very similar to the conventional approach for fabricating wafer-scale silicon AFM probe tips. Process control is feasible and the overall yield is greatly improved. Our method and technology can be easily adapted to many other nanomaterials (nanotubes and nanowires) synthesis and processes for their rational design, fabrication, and integration in their applications.