Scratch-related magnetic signal degradation can occur during magnetic storage hard disk drive operation when the read-write heads contact the spinning multilayer disks. To investigate this phenomenon controlled nanoscratch experiments were performed on perpendicular magnetic recording media using various indenters of different radii of curvature. Various loading conditions were used to cause permanent scratches that were measured using atomic force microscopy. The nanoscratch experiments were simulated using finite element analysis (FEA) that included the detailed nanometer scale thin-film multilayer mechanical properties. The permanently deformed field in the sub-surface magnetic recording layer was extracted from the FEA results. The residual scratch widths measured on the surface of the magnetic storage disk were directly compared with the residual sub-surface widths of the region on the magnetic recording layer where extensive permanent lateral deformation was present. It was found that the sub-surface widths of the deformed regions were significantly larger than the surface scratch widths. Thus, sub-surface thin-film layers, such as the magnetic recording layer could be damaged without observable damage to the protective top surface carbon overcoat. The exact location and extent of damage to the magnetic recording layer depends on the scratch load, size of scratch tip, and the friction at the interface. Such permanent deformation in magnetic recording layer could lead to demagnetization, which has been reported in the literature.