Abstract: Methods and systems for preparing a substrate for analysis are provided. One method includes removing a portion of a copper structure on the substrate using an etch chemistry in combination with an electron beam. The etch chemistry is substantially inert with respect to the copper structure except in the presence of the electron beam. Other methods involve forming masking layers on a substrate that will protect the substrate during etching. For example, one method includes exposing a first portion of the substrate to an electron beam. A second portion of the substrate not exposed to the electron beam includes a copper structure. The method also includes exposing the substrate to a fluorine containing chemical. The fluorine containing chemical bonds to the first portion but not the second portion to form a fluorine containing layer on the first portion.