1. An automatic scan and mark apparatus comprising a machine tool comprising a stage for receiving a specimen with a scraped surface; a movable module controlled to move three-dimensionally with respect to the stage and having a distal end extending toward the stage; a location detection module controlled to detect a position of the movable module; a laser detector having an optical distance sensor, securely mounted on the movable module adjacent to the distal end of the movable module and controlled to measure a surface morphology of the scraped surface; a multi-color ink jet securely mounted on the movable module adjacent to the distal end of the movable module and controlled to eject colored inks toward the scraped surface of the specimen at specific position; and a control computer electronically connected to the location detection module, the laser detector and the ink jet, wherein the control computer controls the location detection module to determine the position of the movable module; the control computer controls the laser detector to detect the surface morphology of the scraped surface in a measurement range; and the control computer activates the ink jet to eject inks on high points of the scraped surface of the specimen.