A method for detecting substructure, comprising the steps of: non-destructively scanning an assembly using a substructure scanning system including a precision motion carriage, wherein the precision motion carriage includes a first probe positioner, a second probe positioner and a frame used to enclose a two-dimensional area, and a non-destructive scanning sensor, wherein the first probe positioner is inserted into the frame, wherein the second probe positioner is inserted in the frame and located above said first probe positioner and, wherein the scanning sensor is inserted into a window formed by a first opening of said first probe positioner and a second opening of said second probe positioner; positioning said assembly including a substructure covered with an outer skin under said substructure scanning system; positioning said scanning sensor on said outer skin of said assembly; moving said scanning sensor over said outer skin across said two-dimensional area using said first probe positioner and said second probe positioner of said precision motion carriage in an x-y raster mode, wherein said first probe positioner is moveable in an x-direction and said second probe positioner is movable in a y-direction within said frame, wherein said scanning sensor is moved by moving said first probe positioner and/or said second probe positioner such that said scanning sensor respectively moves within said second opening of the second probe positioner and/or within said first opening of said first probe positioner; locating said substructure through said outer skin by evaluating signals received from said scanning sensor; controlling an assembly process using said location of said substructure. non-destructively scanning an assembly using a substructure scanning system including a precision motion carriage, wherein the precision motion carriage includes a first probe positioner, a second probe positioner and a frame used to enclose a two-dimensional area, and a non-destructive scanning sensor, wherein the first probe positioner is inserted into the frame, wherein the second probe positioner is inserted in the frame and located above said first probe positioner and, wherein the scanning sensor is inserted into a window formed by a first opening of said first probe positioner and a second opening of said second probe positioner; positioning said assembly including a substructure covered with an outer skin under said substructure scanning system; positioning said scanning sensor on said outer skin of said assembly; moving said scanning sensor over said outer skin across said two-dimensional area using said first probe positioner and said second probe positioner of said precision motion carriage in an x-y raster mode, wherein said first probe positioner is moveable in an x-direction and said second probe positioner is movable in a y-direction within said frame, wherein said scanning sensor is moved by moving said first probe positioner and/or said second probe positioner such that said scanning sensor respectively moves within said second opening of the second probe positioner and/or within said first opening of said first probe positioner; locating said substructure through said outer skin by evaluating signals received from said scanning sensor; controlling an assembly process using said location of said substructure.