Can you please tell us what you mean exactly by slow? Or, in other words, how many bytes (or megabytes, whatever) you're processing per unit of time? And, if possible, how much faster your would expect tor want) it to be?

For finding the slow parts in your program, the best is probably to use a profiling tool such as Devel::NYTProf.

Otherwise, as a general comment, I would suspect that using the regex engine in a loop to fetch one byte at a time is probably quite inefficient. unpack is very likely to be significantly faster if you can use it. Even substr in a loop is quite probably going to run faster.