Method of manufacturing a magnetic read sensor having a low resistance cap structure

A method for manufacturing a magnetic sensor that decreases area resistance and decreases MR ratio of the sensor by eliminating any oxide formation in the capping layer of the sensor. The method includes forming a sensor stack having a multi-layer capping structure formed there-over. The multi-layer capping structure can include first, second, third and fourth layers. The second layer is constructed of a material that is not easily oxidized and which is different from the first layer. The sensor can be formed using a mask that includes a carbon hard mask. After the sensor stack has been formed by ion milling, the hard mask can be removed by reactive ion etching. Then, a cleaning process is performed to remove the second, third and fourth layers of the capping layer structure using an end point detection method such as secondary ion mass spectrometry to detect the presence of the second layer.