An electromagnetic data acquisition system and an associated method for measuring subsurface structures with electromagnetic fields is employed for removing near surface effects from borehole to surface electromagnetic data. Preferably, the system is used to obtain information about deep, target structures located deep below the Earth, especially in oil and gas fields, while mitigating the effect of near surface geological shallow structures on collected electromagnetic (EM) data by using a series of electromagnetic measurements and data treatments that preferentially illuminate near surface geologic shallow structures so that the shallow structures may be recovered separately from deep structures of interest.