An ion beam sample preparation method comprising the steps of: a) directing an ion beam having an intensity and having a first tilt angle toward said sample such that at least a portion of said sample is prepared by said ion beam inside a vacuum chamber; b) illuminating at least a portion of said sample; c) rotating said sample using a rotation stage having a rotation axis that substantially intersects a portion of said ion beam; characterized in the further steps of: d) capturing a substantially focused image of at least a portion of said sample; e) extracting in an instrument controller one or more features from said captured image, characterised in that the one or more features comprises at least one of a color in a portion of said captured image, a shape in a portion of said captured image, or a portion of an optical interference ring in a portion of said captured image; and the method further being characterised in that it comprises the step of: f) responding in said instrument controller to the extraction of said one or more features by performing at least one of: changing the tilt angle of said ion beam to a second tilt angle; or changing the rotation angle of said rotation stage. a) directing an ion beam having an intensity and having a first tilt angle toward said sample such that at least a portion of said sample is prepared by said ion beam inside a vacuum chamber; b) illuminating at least a portion of said sample; c) rotating said sample using a rotation stage having a rotation axis that substantially intersects a portion of said ion beam; characterized in the further steps of: d) capturing a substantially focused image of at least a portion of said sample; e) extracting in an instrument controller one or more features from said captured image, characterised in that the one or more features comprises at least one of a color in a portion of said captured image, a shape in a portion of said captured image, or a portion of an optical interference ring in a portion of said captured image; and the method further being characterised in that it comprises the step of: f) responding in said instrument controller to the extraction of said one or more features by performing at least one of: changing the tilt angle of said ion beam to a second tilt angle; or changing the rotation angle of said rotation stage. d) capturing a substantially focused image of at least a portion of said sample; e) extracting in an instrument controller one or more features from said captured image, characterised in that the one or more features comprises at least one of a color in a portion of said captured image, a shape in a portion of said captured image, or a portion of an optical interference ring in a portion of said captured image; and the method further being characterised in that it comprises the step of: f) responding in said instrument controller to the extraction of said one or more features by performing at least one of: changing the tilt angle of said ion beam to a second tilt angle; or changing the rotation angle of said rotation stage. f) responding in said instrument controller to the extraction of said one or more features by performing at least one of: changing the tilt angle of said ion beam to a second tilt angle; or changing the rotation angle of said rotation stage.