Methods for aligning patterns on a substrate based on optical properties of a mask layer and related devices

A method of aligning patterns on a substrate, comprising:

• forming a first alignment key on the substrate;
• forming a material layer on the first alignment key;
• forming a mask layer on the material layer;
• implanting ions into the mask layer;
• forming a second alignment key on the mask layer;
• and
• optically determining relative locations of the first and second alignment keys through the mask layer after implanting the ions therein.

A semiconductor device, comprising:

• a substrate;
• an alignment key on the substrate;
• a planarized material layer on the alignment key;
• and
• an amorphous carbon mask layer including nitrogen therein on the material layer.