A method of etching a substrate includes providing an etching solution in a tank of an etch processing system, where the etch processing system is configured to control temperature of the etching solution, a concentration of the etching solution, and flow of the etching solution within the tank. The substrate contains micro-fabricated structures that have alternating layers of a first material and a second material, and the etching solution including an acid that etches the first material and results in an etch product to be moved from the substrate. The method further includes monitoring a concentration of the etch product within the etching solution, and maintaining the concentration of the etch product within the etching solution below a predetermined value to prevent deposition of the etch product on the second material in an amount that blocks etching of the first material by the etching solution.