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Transmission electron microscope (TEM) tomography is a useful technique for visualizing threedimensional (3D) structures of materials and nano-devices. A 3D image is reconstructed from a tilt series, which is a set of images collected at different tilt angles over a large angular range. To acquire accurate 3D images, it is important to align precisely the tilt series before reconstruction. A fiducial marker method is a typical method for carrying out alignments [1]. In the method, colloidal gold nano-particles placed by dropping on to the specimen are usually used as markers. For precise alignment, more markers (15 markers are recommended in [1]) must be dispersed suitably over the region of the specimen that is to be observed. However, it is difficult to obtain even dispersion because the colloidal gold nano-particles are usually dense materials. If dense colloidal gold nanoparticles are close to or in contact with the specimen, they introduce artifacts into the reconstructed 3D images, where it might be the case that no marker actually exists. Therefore, it is desired to fabricate the makers on selected area of the specimen by other technique.Beam-induced deposition has been reported as a method for forming nanostructures less than 100 nm in size, and a superiority of using an electron beam compared to a gallium focused ion beam was discussed because of their minimum spot sizes, sub-nanometer and a few nanometer for an electron beam and the gallium ion beam, which limit the minimum size of structures [2]. Recently, a helium ion microscope (HIM) was developed [3]. The beam spot size of the HIM is around 0.25 nm under optimal observation conditions and the maximum distribution energy of the secondary electrons is about 1 eV [4]. Therefore, it is expected that helium ion beam deposition can be used to produce dots of a few nm diameter without any deposition on the periphery of a focused area. This is contrary to what happens when a gallium ion beam is used due to the emission of secondary electrons that have energies higher than a few electron volts. We tried to form nano-dots via position control by using a HIM equipped with a tungsten carbonyl (W(CO) 6 ) gas injection system (GIS). Moreover, we tried for the first time to form dots on a specimen to use them as markers for aligning a TEM tomographic tilt series [5]. It is usually considered that the specimen angles displayed in the TEM control monitor are the correct tilt angles. However, when this assumptions is erroneous, the incorrect angles might induce misalignment [6]. If such a case, it is needed to measure the tilt angles correctly. In a Newton's algorithm which was one process of the fiducial marker method, the tilt angles can be calculated as translational displacements and rotational angles when the tilt angles are treated as unknown values. However, accuracy of the calculation becomes low, if the markers' dispersion in the vertical direction of the tilt axis is not enough as shown in simulation of fig 1. Therefore, we formed markers on a rod-shaped sp...