Method for preparing samples for imaging

An charged particle beam apparatus comprising:

• an ion source;
• a focusing column for focusing the ions onto a work piece in a sample vacuum chamber;
• a gas injection system for providing a precursor gas at the work piece surface;
• a controller for controlling the operation of the charged particle beam system in accordance with stored computer-readable instructions;
• and
• a computer readable memory storing computer instruction for controlling the charged particle beam system to:
• directing an ion beam toward a work piece to remove material and expose a surface, the exposed surface having irregularities;
• depositing material on the exposed surface, the deposited material smoothing the irregularities;
• directing an ion beam toward the work piece to remove the deposited materials and some material from the exposed surface to produce a smooth cross sectional face.