An improved method and apparatus for extracting and handling samples for STEM analysis. Preferred embodiments of the present invention make use of a micromanipulator and a hollow microprobe probe using vacuum pressure to adhere the microprobe tip to the sample. By applying a small vacuum pressure to the lamella through the microprobe tip, the lamella can be held more securely and its placement controlled more accurately than by using electrostatic force alone. By using a probe having a beveled tip and which can also be rotated around its long axis, the extracted sample can be placed down flat on a sample holder. This allows sample placement and orientation to be precisely controlled, thus greatly increasing predictability of analysis and throughput.