Active-source-pixel, integrated device for rapid analysis of biological and chemical specimens

A method for fabricating a sample well and optical structure aligned to the sample well, the method comprising:

• forming, in a same patterning step and in a first layer disposed on a substrate, a first pattern for the sample well and a second pattern for the optical structure, wherein the optical structure is aligned to the sample well;
• etching first features for the optical structure to a first depth into the substrate based on the second pattern;
• etching the sample well to a second depth based on the first pattern;
• covering at least the first pattern of the sample well with a resist layer before etching the first features;
• removing portions of the first layer not covered by the resist layer;
• removing the resist layer;
• depositing a material over the substrate;
• and
• removing a remaining portion of the first layer prior to etching the sample well to the second depth, wherein the second depth is greater than the first depth.