1. A charged particle system having a charged particle beam source, focusing optics for directing the charged particle beam towards a sample, a detector for forming an image of the sample and arrange to perform the method of: repeatedly obtaining an image of the surface layer of the specimen; removing the surface layer of the specimen, thereby bringing the next slice to the surface; and after at least one of the removals of the surface layer the specimen is exposed to a staining agent without the specimen from the system, the staining agent comprises a staining gas or vapor.