The easiest solution (although not the most efficient) would be to invoke Perl from within Perl. For example, use the loops you already have defined to gather a set of path names into an array. Then, invoke:

system('perl', '-I.bak', '-pe', 's[main.php\?page=][/?id=]g', @pathnam
+es) == 0
    or die "Subcommand failed with return code $?.\n";
[download]

Try to make the regexp as accurate and complete as possible to avoid incorrect alterations. If you want a longer term solution that is a bit more efficient, see the perlrun manpage to see an example of the code that approximates the behaviour of -pI.bak.

NOTE: If the above system() invocation does not work, try changing 'perl' to be $^X ($EXECUTABLE_NAME with 'use English'). If the regular expression becomes very complicated, it may be easier to store the command in a perl script, and use the sub-script name instead of -e '...' in the system() invocation.