She skimmed through his letter.

Literal

She [topic-は] he [from-からの] letter [over-に] [briefly-ざっと] eyes-passed.

目を通す ('cast one's eye over, skim') is a set phrase, often paired with ざっと ('roughly, briefly'). The に here marks the surface or domain over which the eyes pass — analogous to English 'glance over.' Together, ざっと目を通す is the standard Japanese for 'give it a quick read.'