High aspect ratio carbon layer etch with improved throughput and process window

A method for patterning a substrate, the method comprising:

• forming a carbon-containing hard mask layer on one or more underlying layers formed on the substrate, wherein a thickness of the carbon-containing hard mask layer is greater than 1 micrometer (μm);
• forming one or more overlying layers above the carbon-containing hard mask layer, the one or more overlying layers comprising at least one silicon-containing layer;
• forming a patterned layer on the one or more overlying layers;
• exposing the substrate to a first plasma to etch exposed portions of the carbon-containing hard mask layer not covered by the patterned layer and create openings in the carbon-containing hard mask layer, wherein the exposed portions of the carbon-containing hard mask layer are partially etched to a first depth, which is less than the thickness of the carbon-containing hard mask layer;
• exposing the substrate to a second plasma containing:
• (a) a boron or silicon-containing precursor gas to form a boron or silicon-containing passivation layer on sidewall surfaces of the openings, and (b) a mask de-clogging gas to remove etch by-products, which are deposited within the openings during the exposure to the first plasma;
• and
• exposing the substrate to the first plasma to continue etching the exposed portions of the carbon-containing hard mask layer to a second depth, which is greater than the first depth.