Managing trench depth in integrated systems

A method for fabricating a photonic integrated circuit, the method comprising:

• forming a plurality of structures within one or more layers deposited over a substrate, the substrate consisting essentially of a first material characterized by a first etching rate;
• forming a plurality of trenches through the one or more layers, the plurality of trenches including:
• a first trench that has a bottom surface on or within the substrate that is covered by a layer of a second material characterized by a second etching rate lower than the first etching rate, and
• a second trench that has a bottom surface on or within the substrate;
• etching two or more trenches of the plurality of trenches simultaneously, including at least the first trench and the second trench, to deepen each of the two or more trenches, where the etching preserves at least a portion of the second material on any of the bottom surfaces of the two or more trenches that were covered by a layer of the second material;
• removing the preserved portion of the second material on any of the bottom surfaces of the two or more trenches that were covered by a layer of the second material;
• and
• after removing the preserved portion of the second material, etching a set of trenches of the plurality of trenches simultaneously, including at least the first trench and the second trench, to deepen each of the trenches of the set of trenches.