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If you mean why must they be square then this is to do with the Tungsten CMP used to fill the contacts and vias which form the tungsten plug. if they were rectangular with a length considerably longer than width this can lead to defects in the CMP process (although some technologies do allow this for a seal ring). If they are allowed to arbitrarily sized, the the tungsten CMP process could cause reliability issues by causing the centre of the tungsten plug to be recessed too far.
If you mean why are they rectangular and not circular, well the answer is they are circular when imaged onto the silicon due to diffraction effects.
They are not draw circular because the GDS software that is the basis of all IC design layouts (for now) is vector based, so to draw a square requires 4 vectros, to draw a circle requires more vectors than I am paid!
This is the lithography guys running into tool tuning limits.
Back in the day, when contacts were >1um, we drew any
old shape we wanted. 3x100um, whatever. But to get good
print yield at small geometry you had best pick one geometry
and tune the hell out of your process.