A metal ion detector with a submicron size electrode was fabricated by field-induced AFM oxidation. The square frame of the mesa pattern was functionalized by APTES for the metal ion detection, and the remaining portion was used as an electrode by the self-assembly of MPTMS for Au metal deposition. The conductance changed with the quantity of adsorbed copper ions, due to electron tunneling between the mobile and surface electrodes. The smaller electrode has a lower limit of detection due to the enhancement in electron tunneling through metal ions that are adsorbed between the conductive-tip (mobile) and the surface (fixed) electrode. This two-electrode system immobilized with different functional groups was successfully used in the selective adsorption and detection of target materials.