Jay's answer is correct, this occurs as a result of Gestalt processing. I will address your comment that:
No response actually brings light on why we prefer things to be aligned, only the realization of such fact (for example, Gestalt
But first I will say that I believe this assumption is wrong:
Nothing in nature is "aligned".
Many things in nature are aligned. The sides of my body are roughly parallel. The same with the sides of my arm, a tree trunk, a river, etc. In fact many Gestalt properties occur so often in nature, that they have been deemed "non-accidental" properties (Lowe, 1987; Witkin &
Tenenbaum, 1983). The idea is that the probability of seeing, e.g., two parallel lines by chance alone would be extremely small if lines in nature had random orientation. But it's not rare, and so it must have some significance (e.g. they are part of the same object).
Jepson and Richards (1992) formalize this argument in a Bayesian framework, and show that statistical regularities in the environment (such as Gestalt features) make good "features" precisely because they are "non-accidental", and thus probably carry informational content.
Richards, W., & Jepson, A. (1992). What makes a good feature? (No.
AIM-1356). MASSACHUSETTS INST OF TECH CAMBRIDGE ARTIFICIAL
INTELLIGENCE LAB. PDF