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Potential field perturbations are investigated as a result of the interactions between the spacer pinholes under the permalloy overlay and the magnetic and stress fields. Considering these interactions, the potential field of a single permalloy bar is calculated, first against permalloy trapping effect, then against in-plane field driving effect, and finally against bias field polarization effect. The calculated potential well is found to have considerable local variations around the pinhole. The overall potential well is also found to be influenced by the pinhole. These perturbations can be further modulated by the mechanical stress field around the pinhole. These effects may cause pinning and/or nucleation of bubbles under the permalloy overlay.