is regex matching the fastest way to go?

Depends. In Perl it probably is, being a well implemented algorithm. In general it's not, since the regex algorithm isn't as fast as the one you find in Unix grep and similar, but is more robust and allows for a lot of clever and powerful matching.

But that's obviously the wrong question, given that a: this looks like a premature optimization, and b: Perl isn't that fast to begin with, due to a lot of stuff that goes behind the scenes which allows for all the flexibility and DWIMability. A better, I believe, course would be to profile the entire program run, see what are the bottlenecks and then figure how to better iron them out, rather than assuming the regex engine will be your biggest problem, rather than, say, Perl's IO.