Providing a columnar structure having a uniform shape and excellent heat resistance and mechanical strength that is formed on a substrate of silicon, a method of preparing the structure, and a DNA separation device prepared by the method. A structure has, on a substrate made of silicon, columns of which main surface is covered with a thermally oxidized film. The columns are made of the thermally oxidized film only or of the thermally oxidized film and silicon. The thermally oxidized film formed on the columns is connected to those formed on the surface or inside of the substrate.