A process and system for determining alignment data for partially obscured 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.