An apparatus for extracting a sample from a substrate, the sample having a planar sample face, and the apparatus comprising: (a) a moveable stage for a semiconductor substrate, the stage connected to one or more stage controllers; (b) a microprobe; (c) a micromanipulator connected to the microprobe, said micromanipulator connected to one or more micromanipulator controllers; (d) a sample holder for holding the extracted sample, said sample holder also mounte on a moveable stage; (e) an optical microscope; and (f) said microprobe comprising a hollow tube with a tip, said microbe connected to a vacuum source and open at said microprobe tip such that a vacuum can be applied through the microbe tip; characterized by: a computer having a memory holding computer-readable instructions, said computer operably connected to said stage controllers, said micromanipulator controllers, and said imaging device; and light source positioned at an oblique angle with respect to the semiconductor substrate surface to illuminate angled walls within a cavity along the semiconductor substrate, the optical microscope for checking the presence or absence of light reflected sequentially off of two opposing angled cavity side walls along a determined path, and in response to the absence, the presence of a sample in a central area of the cavity is determined. (a) a moveable stage for a semiconductor substrate, the stage connected to one or more stage controllers; (b) a microprobe; (c) a micromanipulator connected to the microprobe, said micromanipulator connected to one or more micromanipulator controllers; (d) a sample holder for holding the extracted sample, said sample holder also mounte on a moveable stage; (e) an optical microscope; and (f) said microprobe comprising a hollow tube with a tip, said microbe connected to a vacuum source and open at said microprobe tip such that a vacuum can be applied through the microbe tip; characterized by: a computer having a memory holding computer-readable instructions, said computer operably connected to said stage controllers, said micromanipulator controllers, and said imaging device; and light source positioned at an oblique angle with respect to the semiconductor substrate surface to illuminate angled walls within a cavity along the semiconductor substrate, the optical microscope for checking the presence or absence of light reflected sequentially off of two opposing angled cavity side walls along a determined path, and in response to the absence, the presence of a sample in a central area of the cavity is determined. a computer having a memory holding computer-readable instructions, said computer operably connected to said stage controllers, said micromanipulator controllers, and said imaging device; and light source positioned at an oblique angle with respect to the semiconductor substrate surface to illuminate angled walls within a cavity along the semiconductor substrate, the optical microscope for checking the presence or absence of light reflected sequentially off of two opposing angled cavity side walls along a determined path, and in response to the absence, the presence of a sample in a central area of the cavity is determined.