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We evaluated imaging alteration associated with porphyry copper style mineralisation using aeromagnetic data in the Highland Valley Copper (HVC) district as part of the Natural Sciences and Engineering Research Council of Canada (NSERC) and Canada Mining Innovation Council (CMIC) Footprints project. The first step of the investigation involved construction of a 3D geological model based on surface and regional information, and petrophysical data of the host rocks. From the petrophysics, it was observed that hydrothermal alteration affected the magnetic susceptibility of some batholithic host rocks at HVC, and low susceptibility values were associated with the altered rocks. From this observation, an alteration index was devised, differencing, based on the magnetic susceptibility, between unaltered and altered batholith host rocks. Three-dimensional inversions were conducted using geological constraints obtained from surface and borehole geology as well as physical property data. Then the alteration index methodology was tested using 3D inversions and residual models within five overlapping blocks covering portions of the batholith. The indices inferred from inverted susceptibility were compared to surface mapped alteration. For some felsic facies of the batholith, the alteration index derived from inverted magnetic susceptibility corresponds to the mapped alteration and delineates the known porphyry Cu system district. However, it is not true for others where alteration was less magnetite-destructive and more focused in structures.