Detection and quantification of corrosion damage in aircraft structures is essential for condition based maintenance strategies and for the extension of the life of the aircraft. The eddy current technique was found to be one of the most favorable methods for the determination of thickness loss due to corrosion because this technique is capable of detecting corrosion in several layers of a multi-layer structure. A limitation for the eddy current technique is the eddy current penetration depth. Decreasing the analyzing frequency can increase the eddy current penetration depth. Giant Magneto Resistive sensors are highly sensitive magnetic field sensors, they have better signal to noise ratio for very low frequencies than conventional coils systems. Moreover these sensors are very efficient over a broad frequency range. Hence they allow the use of the multi-frequency concept for multi-layer structures of higher thickness. Images of corrosion damage can be generated separately for different layers of a multi-layer structure by using deep penetrating GMR based eddy current probes and data acquired from the multi-frequency eddy current testing. This paper describes the design of deep penetrating GMR based eddy current probes and their application for generating images of corrosion in different layers with the help of a MAUS scanner.