Sample inspection apparatus, sample inspection method, and sample inspection system are offered which can give a stimulus to a sample held on a film when the sample is inspected by irradiating it with a primary beam (e.g., an electron beam or other charged-particle beam) via the film. The apparatus has the film, a vacuum chamber, primary beam irradiation column, signal detector, and a controller for controlling the operations of the beam irradiation column and signal detector. The sample is held on a first surface of the film opened to permit access to the film. The vacuum chamber reduces the pressure of the ambient in contact with a second surface of the film. The irradiation column irradiates the sample with the primary beam via the film from the second surface side. The detector detects a secondary signal produced from the sample in response to the irradiation.