Over the past three decades, atomic force microscopy (AFM) has undergone a series of design changes to attain a flat XY scan and stable non-contact mode in ambient atmosphere. AFM has evolved into an ideal method for non-destructive scanning of samples with longer probe tip life, high accuracy, repeatability, and automation. Together with self-optimizing algorithms for scan parameters in the non-contact mode, AFM can become as widely adopted as other microscopies such as optical or scanning electron microscopy (SEM). Even full automation of AFM probe tip exchange is now possible with probe type recognition software and laser beam alignment on the cantilever and position-sensitive photo diode (PSPD). By separating the optics stage from the Z stage, an AFM system can be made with low mechanical noise and improved optical vision.