They're both grammatical and they're both used in all registers. It's a style choice. Sometimes one is better than the other. And sometimes there's another choice:
(A) Smallville, the town in which I was raised, was boring.
(B) Smallville, the town where I was raised, was boring.
(C) Smallville, the town I was raised in, was boring.
(A) is a bit stiff and not what most native speakers would say or write in most cases. It's very formal. (B) and (C) are more informal and more frequently.
The sentence you've provided, However, this pros, is limited for the objets where an edge resides perpendicular to the ridge-line and connects via two other edges is both ungrammatical and incomprehensible unless I change two of the words to make it mean something (to me, but but it may be what you want the sentence to say):
However, this process, is limited for the objects where an edge resides perpendicular to the ridge-line and connects via two other edges.
This still has usage, punctuation, and maybe semantic problems. Perhaps it should be this:
However, this process is limited to objects with an edge that is perpendicular to the ridge-line and connects via two other edges.
or this:
However, this process is limited for objects with an edge that is perpendicular to the ridge-line and connects via two other edges.