3-dimensional observation is carried out on the atomic arrangement and atomic species in a thin-film specimen at an atomic level in order to clarify the existence states of defects and impure atoms in the crystals. For that purposes, the present invention provides an instrument and a method for 3-dimensional observation of an atomic arrangement which are implemented by a system comprising a scanning transmission electron microscope equipped with a field emission electron gun operated at an acceleration voltage of greater than 200 kV, a specimen goniometer/tilting system having a control capability of the nanometer order, a multi-channel electron detector and a computer for executing software for controlling these components and 3-dimensional image-processing software. Point defects and impure atoms, which exist in joint interfaces and contacts in a ULSI device, can thereby be observed. As a result, the causes of bad devices such as current leak and poor voltage resistance can be analyzed at a high accuracy.