The present invention provides methods for etching a quartz substrate using a second level photoresist layer disposed thereon as an etching mask. In one embodiment, a method of etching a quartz substrate for forming a photomask includes providing a quartz substrate having a metal containing layer disposed thereon in an etch chamber, applying a first photoresist layer on a substrate, patterning the first photoresist layer to remove a first region of the metal containing layer to expose a first portion of the quartz substrate while remaining a second region of the metal containing layer on the quartz substrate, removing the remaining first photoresist layer on the quartz substrate, applying a second photoresist layer on the exposed quartz substrate and the second region of the metal containing layer, patterning the second photoresist layer to form openings in the second photoresist layer exposing the underlying quartz substrate, and etching the quartz substrate defined by the patterned second photoresist layer.
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