An ion beam apparatus for preparing a sample comprising: an ion beam irradiating means disposed in a vacuum chamber and configured to direct a broad ion beam along a central ion beam axis; a beam probe attached to the ion beam irradiating means; the broad ion beam comprising: a working portion directed toward said sample; and a monitoring portion directed toward the beam probe, said ion beam irradiating means being a modulating ion beam irradiating means configured to provide one or more ion beam characteristics comprising at least one of: i. an instantaneous current of ions; ii. an instantaneous flux of ions; iii. an instantaneous flux of neutrals; iv. a time-averaged current of ions; v. a time-averaged flux of ions; vi. a time-averaged flux of neutrals; vii. an integrated current of ions; viii. an integrated flux of ions; ix. an integrated flux of neutrals; x. an instantaneous energy of ions; xi. a time-averaged energy of ions; xii. an integrated energy of ions; xiii. an instantaneous energy distribution of ions; xiv. a time-averaged energy distribution of ions; and, xv. an integrated energy distribution of ions; said working portion having one or more working portion characteristics from said one or more ion beam characteristics; wherein said monitoring portion has one or more monitoring portion characteristics selected from said list of said ion beam characteristics; a sample retention stage configured to retain said sample in a predetermined position and orientation with respect to the central ion beam axis; the beam probe disposed to receive said monitoring portion of the broad ion beam; wherein said beam probe is configured to receive said monitoring portion substantially without altering said working portion of said broad ion beam; wherein said beam probe is configured to produce a probe signal responsive to one or more monitoring portion characteristics; wherein said ion beam irradiating means is responsive to receiving said probe signal by modulating said one or more ion beam characteristics or terminating the broad ion beam; wherein the position and direction of said ion beam irradiating means may be changed so that the angle of incidence of the central ion beam axis to the sample may be changed; and wherein the beam probe is disposed in relation to the ion beam irradiating means such that a monitoring portion received by beam probe and having one or more monitoring portion characteristics is substantially unaffected by a tilt angle of the ion beam. an ion beam irradiating means disposed in a vacuum chamber and configured to direct a broad ion beam along a central ion beam axis; a beam probe attached to the ion beam irradiating means; the broad ion beam comprising: a working portion directed toward said sample; and a monitoring portion directed toward the beam probe, said ion beam irradiating means being a modulating ion beam irradiating means configured to provide one or more ion beam characteristics comprising at least one of: i. an instantaneous current of ions; ii. an instantaneous flux of ions; iii. an instantaneous flux of neutrals; iv. a time-averaged current of ions; v. a time-averaged flux of ions; vi. a time-averaged flux of neutrals; vii. an integrated current of ions; viii. an integrated flux of ions; ix. an integrated flux of neutrals; x. an instantaneous energy of ions; xi. a time-averaged energy of ions; xii. an integrated energy of ions; xiii. an instantaneous energy distribution of ions; xiv. a time-averaged energy distribution of ions; and, xv. an integrated energy distribution of ions; i. an instantaneous current of ions; ii. an instantaneous flux of ions; iii. an instantaneous flux of neutrals; iv. a time-averaged current of ions; v. a time-averaged flux of ions; vi. a time-averaged flux of neutrals; vii. an integrated current of ions; viii. an integrated flux of ions; ix. an integrated flux of neutrals; x. an instantaneous energy of ions; xi. a time-averaged energy of ions; xii. an integrated energy of ions; xiii. an instantaneous energy distribution of ions; xiv. a time-averaged energy distribution of ions; and, xv. an integrated energy distribution of ions; said working portion having one or more working portion characteristics from said one or more ion beam characteristics; wherein said monitoring portion has one or more monitoring portion characteristics selected from said list of said ion beam characteristics; a sample retention stage configured to retain said sample in a predetermined position and orientation with respect to the central ion beam axis; the beam probe disposed to receive said monitoring portion of the broad ion beam; wherein said beam probe is configured to receive said monitoring portion substantially without altering said working portion of said broad ion beam; wherein said beam probe is configured to produce a probe signal responsive to one or more monitoring portion characteristics; wherein said ion beam irradiating means is responsive to receiving said probe signal by modulating said one or more ion beam characteristics or terminating the broad ion beam; wherein the position and direction of said ion beam irradiating means may be changed so that the angle of incidence of the central ion beam axis to the sample may be changed; and wherein the beam probe is disposed in relation to the ion beam irradiating means such that a monitoring portion received by beam probe and having one or more monitoring portion characteristics is substantially unaffected by a tilt angle of the ion beam.