System for performing in-line nanoprobing on semiconductor wafer. A wafer support or vertical wafer positioner is attached to a wafer stage. An SEM column, an optical microscope and a plurality of nanoprobe positioners are all attached to the ceiling. The nanoprobe positioners have one nanoprobe configured for physically contacting selected points on the wafer. A force (or touch) sensor measures contact force applied by the probe to the wafer (or the moment) when the probe physically contacts the wafer. A plurality of drift sensors are provided for calculating probe vs. wafer alignment drift in real-time during measurements.