Embodiments provided herein generally relate to methods of modifying portions of layer stacks. The methods include forming deep trenches and narrow trenches, such that a desirably low voltage drop between layers is achieved. A method of forming a deep trench includes etching portions of a flowable dielectric, such that a deep metal contact is disposed below the deep trench. The deep trench is selectively etched to form a modified deep trench. A method of forming a super via includes forming a super via trench through a second layer stack of a layer superstack. The methods disclosed herein allow for decreasing the resistance, and thus the voltage drop, of features in a semiconductor layer stack.