An etching process is employed to selectively pattern the top magnetic film layer, the tunnel barrier, and the pinned bottom magnetic layer of a magnetic thin film structure. The pinned bottom magnetic film layer has an antiferromagnetic layer or a Ru spacer formed thereunder. The etching process employs various etching steps that selectively remove various layers of the magnetic thin film structure stopping on the antiferromagnetic layer or the Ru spacer. The progress of this etching process can be monitored by measuring the electrochemical potential difference of a part or wafer containing a magnetic structure with respect to a reference electrode simultaneously with the selective etching process.