A method for automated sample preparation in a charged particle beam system, comprising: loading a work piece into a vacuum chamber having one or more charged particle beam systems (3002, 3021) and a sample manipulation probe; removing material surrounding a thin section of the work piece using a focused ion beam leaving the thin section attached to the bulk work piece by small attachment structures; shaping the tip of a sample manipulator probe into a machine-recognizable shape by removing material from the tip using the focused ion beam; using the machine-recognizable shape of the tip to determine the position of the tip relative to the thin section; using the position of the tip relative to the thin section, automatically moving the sample probe sufficiently close to the thin section to attach the manipulator probe using charged particle beam-induced deposition; attaching the sample probe to the thin section; severing said small attachment structures so that the thin section is supported only by the sample probe; moving the sample probe automatically so that the thin section is sufficiently close to a sample grid for holding thin samples to attach the thin section to the sample grid using charged particle beam-induced deposition; attaching the thin section to the sample grid; and removing the tip of the sample probe from the thin section, characterized in that said shaping step includes automatically shaping the probe including a needle, a tip extending from the needle and having a diameter smaller than that of the needle, and a shoulder between the needle and the tip, the method comprising: locating the end of the tip; locating the shoulder; locating a desired tip start position along the needle so that the distance from the desired tip start position to the end of the tip corresponds to a desired tip length; automatically removing with the ion beam first material from the needle from the desired tip start position to at least the shoulder; automatically milling with the ion beam to produce smooth surface from the tip start position to the end of the tip; rotating the manipulator; automatically removing with the ion beam second material from the needle from the desired tip start position to at least the shoulder; and automatically milling with the ion beam to produce a smooth surface from the tip start position to the end of the tip. loading a work piece into a vacuum chamber having one or more charged particle beam systems (3002, 3021) and a sample manipulation probe; removing material surrounding a thin section of the work piece using a focused ion beam leaving the thin section attached to the bulk work piece by small attachment structures; shaping the tip of a sample manipulator probe into a machine-recognizable shape by removing material from the tip using the focused ion beam; using the machine-recognizable shape of the tip to determine the position of the tip relative to the thin section; using the position of the tip relative to the thin section, automatically moving the sample probe sufficiently close to the thin section to attach the manipulator probe using charged particle beam-induced deposition; attaching the sample probe to the thin section; severing said small attachment structures so that the thin section is supported only by the sample probe; moving the sample probe automatically so that the thin section is sufficiently close to a sample grid for holding thin samples to attach the thin section to the sample grid using charged particle beam-induced deposition; attaching the thin section to the sample grid; and removing the tip of the sample probe from the thin section, characterized in that said shaping step includes automatically shaping the probe including a needle, a tip extending from the needle and having a diameter smaller than that of the needle, and a shoulder between the needle and the tip, the method comprising: locating the end of the tip; locating the shoulder; locating a desired tip start position along the needle so that the distance from the desired tip start position to the end of the tip corresponds to a desired tip length; automatically removing with the ion beam first material from the needle from the desired tip start position to at least the shoulder; automatically milling with the ion beam to produce smooth surface from the tip start position to the end of the tip; rotating the manipulator; automatically removing with the ion beam second material from the needle from the desired tip start position to at least the shoulder; and automatically milling with the ion beam to produce a smooth surface from the tip start position to the end of the tip.