Refactoring is an ongoing practice. You should be constantly doing it every time you code. Whenever you end up with three routines that do basically the same thing they should get replaced. (Perl offers a wide reange of ways to do this intelligently, from code generation, to closures, to complex argument handling schemes.) You shouldn't have any global variables. Either encapsulate that data into an object, or pass it as required as parameters.

Without seeing your code in depth, and the problem space it operates in we cant suggest anything solid. Its a skill you learn, where to put data and routines, what modularizes nicely, what doesnt. Expect to get it wrong a few times. Its not uncommon for me to rewrite from scratch the same body of code two or three or even four times before I'm happy with the design.