A method is disclosed for aligning structures on first and second opposite sides of a wafer. First one or more transparent islands are formed on the first side of the wafer at an alignment location. The transparent islands have an exposed front side and a rear side embedded in the wafer. At least one alignment mark is formed on the front side of the transparent island. An anisotropic etch is performed through the second side of said the to form an opening substantially reaching the back side of the transparent island. A precise alignment is then carried out on the alignment mark through the opening and the transparent island. In this way a very precise alignment can be carried out on the back side of the wafer for manufacturing MEMS structures.