Canon 1D X II has a
20.0MP Full frame (36 x 24 mm ) sized CMOS sensor and features Dual DIGIC 6+ processor. On the other hand, 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.
One other difference between these two cameras that is worth mentioning is that Fujifilm X-T1 IR's sensor doesn't have an 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 moiré occurring in certain scenes.
Below you can see the 1D X MII and X-T1 IR sensor size comparison.
As seen above, Canon 1D X II 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.