A method for sample examination in a dual-beam FIB calculates a first angle as a function of second, third and fourth angles defined by the geometry of the FIB and the tilt of the specimen stage. A fifth angle is calculated as a function of the stated angles, where the fifth angle is the angle between the long axis of an excised sample and the projection of the axis of the probe shaft onto the X-Y plane. The specimen stage is rotated by the calculated fifth angle, followed by attachment to the probe tip and lift-out. The sample may then be positioned perpendicular to the axis of the FIB electron beam for STEM analysis by rotation of the probe shaft through the first angle.