The authors demonstrated successful nanopatterning using a high resolution lattice image obtained by transmission electron microscopy (TEM) as a mask signal [H. S. Lee , Adv. Mater. (Weinheim, Ger.) 19, 4198 (2007)]. In this process, the quality of the patterning result is critically dependent on the lattice image, which, in turn, is critically dependent on the quality of the mask. It is often noted that the quality of the mask prepared by the conventional TEM sample preparation technique is far from perfect, which critically limits the quality of patterning. In this work, they first discuss the various origins of the noise signal generated by the mask and then introduce a special type of objective aperture (noise reduction aperture) to remove the noise signal. The effect of the noise reduction aperture, designed for the Si [110] zone axis, is experimentally demonstrated.