A sample preparation system in which an ion beam is made to hit the surface of a sample while rotating the sample about an axis perpendicular to the processed surface of the sample under the condition where the processed surface of the sample is not perpendicular to the beam. The preparation system has a rotating mechanism and a tilting mechanism both of which are mounted in an enclosure mounted to the vacuum chamber. The rotating mechanism rotates the holder about the X-axis perpendicular to the surface of the holder on which the sample is placed. The tilting mechanism tilts the holder about the Y-axis perpendicular to the X-axis.