Abstract: By using focused ion beam-scanning electron microscopy to improve the traditional method of transmission electron microscopy sample preparation. By changing the area and effect of ion beam assisted deposition, and improving the U-shaped cut to L-shaped cut, the compressed mouse bone micro-pillars samples were successfully extracted onto a dedicated copper mesh. The extracted sample could be precisely thinned by ion beam, and the direction of collagen fibers could be observed under transmission electron microscopy.