An automatic scan and mark apparatus has a machine tool, a location detection module, a laser detector, an ink jet and a control computer. The machine tool has a movable module and a stage. The stage mounts and holds a specimen having a scraped surface. The control computer controls the location detection module to determine a position of the movable module, controls the laser detector to detect a surface morphology of the scraped surface in a measurement range, and activates the ink jet to eject inks on high points of the scraped surface of the specimen. Thus, the surface morphology is built automatically and high points are screened out and marked by colored ink. Manufacturer may easily redo scraping of determined high points based on the marked location on the specimen without burdensome measurement.