An improved process flow for an atomic resolution storage (ARS) system deposits conductive electrodes, together with a protective layer, on a media side of a rotor wafer before most of other device processing, thus preserving a surface for ARS storage media from subsequent wafer thinning process. CMOS circuitry is also formed in a stator wafer at a later stage. Therefore, the CMOS circuitry is less likely to be damaged by heat processing. In addition, processing of the media side of the rotor wafer may be performed with loosened thermal budget. Finally, because the media side of the rotor wafer is processed before wafer bonding of the rotor wafer and the stator wafer, there is less probability of degradation of the wafer bonding. Therefore, device yield may be enhanced, leading to lower manufacturing cost.