A method of preparing a sample for TEM analysis, the method comprising: loading a substrate into an ion beam system; separating a sample from the substrate by ion beam milling; extracting the sample from the substrate, said sample having a vertical axis, a top side, and a bottom side, in which the top side is the upper portion of the sample oriented toward the surface of the substrate closest to the ion beam source prior to extraction of the sample, and in which the bottom side is the lower portion of the sample oriented away from the surface of the substrate closest to the ion beam source prior to extraction of the sample; attaching the sample to a sample holder; characterized by: before thinning the sample: positioning (210, 214) the sample holder so that the ion beam is transverse to the vertical axis of the sample; milling the bottom side of the sample to remove at least a portion of the bottom surface of the sample to produce a uniformly flat surface; subsequent to milling the bottom side of the sample to remove at least a portion of the bottom surface of the sample to produce a uniformly flat surface: positioning the sample holder so that the bottom side of the sample is oriented toward the ion beam source and so that the ion beam is parallel to the vertical axis of the sample; thinning the sample by directing the ion beam in a milling pattern that thins at least a portion of the sample to a thickness of 30nm or less. loading a substrate into an ion beam system; separating a sample from the substrate by ion beam milling; extracting the sample from the substrate, said sample having a vertical axis, a top side, and a bottom side, in which the top side is the upper portion of the sample oriented toward the surface of the substrate closest to the ion beam source prior to extraction of the sample, and in which the bottom side is the lower portion of the sample oriented away from the surface of the substrate closest to the ion beam source prior to extraction of the sample; attaching the sample to a sample holder; before thinning the sample: positioning (210, 214) the sample holder so that the ion beam is transverse to the vertical axis of the sample; milling the bottom side of the sample to remove at least a portion of the bottom surface of the sample to produce a uniformly flat surface; positioning (210, 214) the sample holder so that the ion beam is transverse to the vertical axis of the sample; milling the bottom side of the sample to remove at least a portion of the bottom surface of the sample to produce a uniformly flat surface; subsequent to milling the bottom side of the sample to remove at least a portion of the bottom surface of the sample to produce a uniformly flat surface: positioning the sample holder so that the bottom side of the sample is oriented toward the ion beam source and so that the ion beam is parallel to the vertical axis of the sample; thinning the sample by directing the ion beam in a milling pattern that thins at least a portion of the sample to a thickness of 30nm or less. positioning the sample holder so that the bottom side of the sample is oriented toward the ion beam source and so that the ion beam is parallel to the vertical axis of the sample; thinning the sample by directing the ion beam in a milling pattern that thins at least a portion of the sample to a thickness of 30nm or less.