Atomic Energy of Canada Limited (AECL) has been conducting detailed geological, geophysical and geotechnical investigations in plutonic rocks at several research areas. The main focus of the work was on developing and testing site evaluation and site characterization methods to investigate progressively smaller volumes of plutonic rocks in greater details. In this process extremely detailed airborne, surface and borehole geophysical surveys were done to identify fractures and understand groundwater flow conditions. A brief review of geophysical methods, which demonstrate the area scale, site scale and vault scale characterization techniques has been included in this paper. The boreholes in the Whiteshell Research Area (WRA) of Lac du Bonnet Batholith and at its Underground Research Laboratory (URL) excavated to 420 m depth have provided extensive opportunities to develop and test these methods. One example of geophysical surveys associated with the Moderately Fractured Rock (MFR) experiment at 240 Level is discussed in some length.