An interferometric-spatial-phase imaging (ISPI) system includes a substrate wafer. An alignment configuration is permanently embedded in the substrate wafer. The alignment configuration uses a global coordinate reference system by providing a plurality of global reference marks that encompass up to the entire substrate wafer. A plurality of alignment markings is provided on a surface in close proximity to the alignment configuration for obtaining continuous six-axis control to provide positional information of a scanning probe tip or an electron beam with respect to said global coordinate reference system.