Your proposed initial phrase is semantically ambiguous. It is unclear whether you intend having to have a possessive sense ('because [something] has edges which are rectified') or acts as the head of a perfect construction ('because [somebody] has rectified the edges').
In either case, an initial participle phrase like this is obliged to modify the subject of the following main clause, which acts as the 'somebody' or 'something' in my paraphrases. I'm not sure what you mean by 'fixing of boundary', but I doubt that it is either the 'possessor' or the agent of the rectification.
I think what you probably mean is something like
Once the edges have been rectified, the [?fixed boundary?] is more stable and geometrically acceptable.
Once the edges have been rectified, the boundary may be fixed in a more stable and geometrically acceptable position.
If you really want to use the participle construction, it should be like this, with the particpial modifying the subject:
Having rectified the edges, we may fix the boundary in a more stable and geometrically acceptable position.