In a method for fabricating a nanometer-scale structure by arranging nanotubes in a predetermined direction at a predetermined position, the method for fabricating a nanometer-scale structure comprises a first step of planarizing a substrate by etching a predetermined part by irradiating a focused energy beam to the sample, a second step of decomposing and depositing an organic gas into a columnar structure with an objective of determining the position and direction, and a third step of attaching and fixing the nanotube by using the thus deposited columnar structure as a standard of position and direction.