In one embodiment, a sample processing method includes placing a sample on a sample placing module, and setting first processing boxes on one side of slice formation scheduled regions of the sample, and second processing boxes on the other side thereof. The method includes processing the sample by performing a primary scan which sequentially scans the first processing boxes with a continuously generated ion beam, and a secondary scan which sequentially scans the second processing boxes with a continuously generated ion beam, to form slices of the sample. The primary and secondary scans are performed so that a first scanning condition for scanning first regions within the first and second processing boxes is set different from a second scanning condition for scanning second regions between the first processing boxes and between the second processing boxes, to allow frame portions of the sample to remain in the second regions.
