A method for aligning an opaque, active device in a semiconductor structure includes forming an opaque layer over an optically transparent layer formed on a lower metallization level, the lower metallization level including one or more alignment marks formed therein. A portion of the opaque layer is patterned and opened corresponding to the location of the one or more alignment marks in the lower metallization level so as to render the one or more alignment marks optically visible. The opaque layer is then patterned with respect to the lower metallization level, using the optically visible one or more alignment marks.