Fujifilm X-T1 IR has a 16.0MP APS-C (23.6 x 15.6 mm ) sized CMOS X-TRANS II sensor and features EXR Processor II processor. On the other hand, Nikon D3 has a 12.0MP Full frame (36 x 23.9 mm ) sized CMOS sensor and features Expeed processor.
Another difference between these two cameras is that Fujifilm X-T1 IR's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the X-T1 IR and D3 sensor size comparison.
As seen above, Nikon D3 has a 2.3x Larger sensor area than Fujifilm X-T1 IR. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.