We successfully developed a high-precision wafer alignment and bonding system for the fabrication of a variety of 3-D nanostructures. To control the wafer positions with high accuracy during the wafer-bonding process, we improved upon a design of the conventional mask-alignment stage. A stress sensor was incorporated to measure the load between the two wafers. In addition, the parallelism of the wafers was monitored by an optical interferometry system. To determine alignment errors in both the x and y directions simultaneously, we devised an alignment method consisting of crossed vernier scales. We demonstrated that the new alignment and bonding system allowed us to realize precise 3-D photonic crystals with the alignment inaccuracy of < 100 nm at most, and we show that the best experimental error achieved to date was < 25 nm. As this system has the benefit of more readily and intuitively determining the absolute positions of the two wafers, it can be applied to the fabrication of a wide variety of nanoscale multilayer devices.