1. A method of determining feature position data to be used for alignment of a sample to a substrate by employing a tool including a sample holder, a substrate holder and an optical recognition system by the steps as follows: employing identification of an exact or approximate location of a feature of said sample that is at least partially obscured by varying the depth of focus of said optical system upon a feature on said sample; and obtaining and determining a Signal to Noise Ratio (SNR) approximating a maximum value from an image captured by optical means scanning of a feature on said sample.