We demonstrate selective electrodeposition of Pd into atomic force microscopy (AFM) nanoscratches produced in thermal oxide covered p-type Si(100) without creating substantial damage in the silicon substrate. A 10 nm thick thermal SiO2 film was scratched about 5-7 nm deep with a diamond tip of an AFM. Then, etching in HF was used to remove uniformly 4-5 nm SiO2, thus to expose the Si within the nanoscratches while still maintaining an oxide layer on the rest of the surface. Pd was selectively electrodeposited into these scratches. The underlying silicon exhibits no significant damage induced by scratching. (C) 2004 The Electrochemical Society.