Disclosed are apparatus and methods for determining process or structure parameters for semiconductor structures. A plurality of optical signals is acquired from one or more targets located in a plurality of fields on a semiconductor wafer. The fields are associated with different process parameters for fabricating the one or more targets, and the acquired optical signals contain information regarding a parameter of interest (POI) for a top structure and information regarding one or more underlayer parameters for one or more underlayers formed below such top structure. A feature extraction model is generated to extract a plurality of feature signals from such acquired optical signals so that the feature signals contain information for the POI and exclude information for the underlayer parameters. A POI value for each top structure of each field is determined based on the feature signals extracted by the feature extraction model.