Mark protection with transparent film

An alignment system for aligning a substrate and a mask for lithographic processing to thereby minimize registration error between layers of a process structure residing on the substrate, comprising:

• a light source for generating an alignment light;
• a lens located within an optical path of the alignment light, wherein the lens captures diffracted orders of the alignment light which has reflected off of a portion of the substrate and focuses the reflected alignment light upon a grating structure on the mask;
• a plurality of alignment marks at the portion of the substrate;
• a cap overlying the alignment marks on the substrate, wherein the cap is substantially transparent with respect to the alignment light and protects an integrity of the alignment marks from process-induced damage and substantially prevents a generation of noise in the reflected alignment light;
• and
• means for moving the substrate and mask with respect to one another and means for detecting the reflected alignment light, wherein the means for moving adjusts a relative positioning between the mask and the substrate in response to the detected reflected alignment light, thereby establishing an alignment between the mask and the substrate.