Automated systems and methods for processing substrates are described. An automated processing system includes: a vacuum chamber; a substrate support located inside the vacuum chamber and constructed and arranged to support a substrate during processing; and a substrate alignment detector constructed and arranged to detect if the substrate is misaligned as the substrate is transferred into the vacuum chamber based upon a change in a physical condition inside the system. The substrate alignment detector may include a vibration detector coupled to the substrate support. A substrate may be transferred into the vacuum chamber. The position of the substrate may be recorded as it is being transferred into the vacuum chamber. Misalignment of the substrate with respect to the substrate support may be detected. The substrate may be processed. The processed substrate may be unloaded from the vacuum chamber. The position of the processed substrate may be recorded as it is being unloaded from the vacuum chamber. Any substrate misalignment may be compensated for based upon the difference in the recorded substrate positions.