It's a complete sentence.
[introductory adverbial clause], flap (subject) was trimmed (verb) ...
After a few loose 2-0 Vicryl sutures were used, the fifth toe rotation flap was trimmed to fit the base of both the fourth and fifth previous digits.
Question: not a run-on-
not a comma splice
not a complete sentence
Answer:
Thinking it is a fragment (missing a subject).
2 answers
The subjects are "sutures" and "flap." If I was acquainted with the context and terms, it might not seem to run-on. It would seem clearer in two sentences.