An apparatus for performing automated in-situ lift-out of a sample from a specimen includes a computer having a memory with computer-readable instructions, a stage for a specimen and a nano-manipulator. The stage and the nano-manipulator are controlled by motion controllers connected to the computer. The nano-manipulator has a probe tip for attachment to samples excised from the specimen. The computer-readable instructions include instructions to cause the stage motion controllers and the nano-manipulator motion controllers, as well as an ion-beam source, to automatically perform in-situ lift-out of a sample from the specimen.