An improved process workflow and apparatus for S/TEM sample preparation and analysis is provided. Preferred embodiments provide improved methods for an automated recipe TEM sample creation, especially for small geometry TEM lamellae, employing CAD data to automatically align various stages of sample preparation. The process automatically verifies and aligns the position of FIB-created fiducials by masking off portions of acquired images, and then comparing them to synthesized images from CAD data. SEM beam positions are verified by comparison to images synthesized from CAD data. FIB beam position is also verified by comparison to already-aligned SEM images, or by synthesizing an FIB image from CAD using techniques for simulating FIB images. The automatic alignment techniques herein allow creation of sample lamellas at specified locations without operator intervention.