The invention refers to an apparatus (10) for inspecting a sample (12) of a specimen (14) by means of an electron beam (34) comprising a vacuum chamber (18); an ion beam device (20) for generating an ion beam (22) used for etching a sample (12) from the specimen (14) within said vacuum chamber (18); an electron beam device (30) having a scanning unit (32) for scanning the electron beam (34) across said specimen (14) within said vacuum chamber (18); said electron beam device (30) having a first detector (36) positioned to detect electrons (38) that are released from the specimen (14) in a backward direction with respect to the direction of the electron beam (34); and said electron beam device (30) having a second detector (40) positioned to detect electrons (42) that are released from the sample (12) of the specimen (14) in a forward direction with respect to the direction of the electron beam (34); and separation means (50; 52) within said vacuum chamber (18) to separate the sample (12) from the specimen (14) for the inspection of the sample (12) by means of the second detector (40). With the apparatus according to the invention, it is possible to perform a transmission inspection of a sample of a specimen, e.g. a thin slice of a semiconductor wafer, at a high throughput at comparably low costs.