A method and apparatus for processing a specimen with two or more particle beams, wherein the specimen has a milled side that is processed by a first particle beam and observed by a second particle beam. The specimen is milled during a first milling operation by the first particle beam with the specimen in a first position. Thereafter, the specimen tilts in a second position around an axis of tilt of the specimen. Thereafter, the specimen is milled during a second milling operation. Milling can be performed during continuous tilting of the specimen around the axis of tilt. The axis of tilt of the specimen intersects the milled side. In all the aforementioned positions of the specimen, the second particle beam impinges on the milled side, which enables monitoring of the milling in real time.