A method for patterning a layer at a bottom of a high aspect ratio feature of a substrate is described. The method includes providing the substrate having a first layer with a feature pattern overlying a second layer. The feature pattern is characterized with an initial critical dimension (CD), an initial corner profile, and an aspect ratio of 5:1 or greater. The method further includes etching through at least a portion of the second layer at the bottom of the feature pattern to extend the feature pattern at least partially into the second layer while retaining a final CD within a threshold of the initial CD and a final corner profile within a threshold of the initial corner profile using a gas cluster ion beam (GCIB) etching process.