The single component 3M spot putty (or glazing putty) in the tubes are a lacquer based product that is prone to absorbtion of paint solvents and then shrinkage over time. Depending on the size/depth of the scratch, it may shrink enough under the topcoats that a depression is noticeable in the paint, showing exactly where the scratch is. You would be better served with a catalyzed product (2 component) that is not prone to those shrinking issues, such as Evercoat 416.
