Methods and apparatus for efficiently analyzing defects in-line on a wafer by wafer basis are provided. In general terms, embodiments of the present invention provide a simple interface for setting up the entire inspection and defect analysis process in a single set up procedure. The apparatus includes an inspection station for inspecting a specimen for potential defects and a review station for analyzing a sample of the potential defects to determine a classification of such potential defects. The apparatus further includes a computer system having an application interface operable to allow a user to set up the inspection station and the review station during a same setup phase so as to allow the inspection station and the review station to then operate automatically to provide defect information for one or more specimens based on the user set up.