A method of aligning a thin film in a Transmission Electron Microscope, the Transmission Electron Microscope comprising: • an electron source for producing a beam of electrons, • a condenser system for forming a parallel or almost parallel beam of electrons on a sample plane, • an objective lens for focusing the parallel or almost parallel beam on the diffraction plane, • a thin film positioned in or close to the diffraction plane or a plane conjugated thereto, the thin film being a featureless thin film, • an imaging system (116 + 118) for forming an enlarged image of the sample plane or the diffraction plane onto an image plane, • a detector for recording images formed on the image plane, characterized in that the method comprises the steps of • a step of focusing the condenser system with a first excitation associated with a first position of the diffraction plane, • a step illuminating the thin film with the focused beam of electrons, • repeatedly o a step recording an image, o a step in which from said recorded image it is derive whether the illumination is an on-plane illumination or an off-plane illumination, the on-plane illumination occurring when the thin film is located in the diffraction plane or a plane conjugated thereto and the off-plane illumination occurring when the thin film is located in a plane that does not coincide with the diffraction plane or a plane conjugated thereto, o a step of changing the excitation of at least one lens to change the position of the diffraction plane or a plane conjugate thereto or changing the position of the thin film along the optical axis, • until the illumination is an on-plane illumination. • an electron source for producing a beam of electrons, • a condenser system for forming a parallel or almost parallel beam of electrons on a sample plane, • an objective lens for focusing the parallel or almost parallel beam on the diffraction plane, • a thin film positioned in or close to the diffraction plane or a plane conjugated thereto, the thin film being a featureless thin film, • an imaging system (116 + 118) for forming an enlarged image of the sample plane or the diffraction plane onto an image plane, • a detector for recording images formed on the image plane, • a step of focusing the condenser system with a first excitation associated with a first position of the diffraction plane, • a step illuminating the thin film with the focused beam of electrons, • repeatedly o a step recording an image, o a step in which from said recorded image it is derive whether the illumination is an on-plane illumination or an off-plane illumination, the on-plane illumination occurring when the thin film is located in the diffraction plane or a plane conjugated thereto and the off-plane illumination occurring when the thin film is located in a plane that does not coincide with the diffraction plane or a plane conjugated thereto, o a step of changing the excitation of at least one lens to change the position of the diffraction plane or a plane conjugate thereto or changing the position of the thin film along the optical axis, o a step recording an image, o a step in which from said recorded image it is derive whether the illumination is an on-plane illumination or an off-plane illumination, the on-plane illumination occurring when the thin film is located in the diffraction plane or a plane conjugated thereto and the off-plane illumination occurring when the thin film is located in a plane that does not coincide with the diffraction plane or a plane conjugated thereto, o a step of changing the excitation of at least one lens to change the position of the diffraction plane or a plane conjugate thereto or changing the position of the thin film along the optical axis, • until the illumination is an on-plane illumination.