a process and system for determining alignment data for features on wafers or chips when a wafer or chip is substantially coated by an over bump applied material , e . g . a resin or film , and using that data to align the wafers or chips for subsequent operations such as dicing or joining . position data for alignment is produced by identifying a location of an at least partially obscured feature by varying the depth of focus upon a work piece to determine an snr approximating a maximum value from an image captured by optical scanning . an snr above a threshold value can be employed .