What do you mean by "compiling"? Perl's compiler is part of the interpreter, simply running a script first compiles it and then runs it (and sometimes switches between the two phases to and fro). Makefile.PL and Build.PL are used to install modules, sometimes compilation could be ivolved (but it's usually XS, i.e. C, that's being compiled).
What exactly are you doing? What are you trying to achieve?