Found an example of an regexp to do this in perldoc perlre, and implemented it. should work.

#!perl -l

use strict;

my @a=("func2(func1(input1, input2), input3)", "func1(input1, func2(in
+put2, input3))");
my $re = "";
$re=qr{\((((?>[^()]+)|(??{ $re }))*)\)};

for my $line (@a) {
    $line =~ s/func1$re/proc1{$1}/g;
    $line =~ s/func2$re/FUNC $1 END/g;
    $line =~ tr/{}/()/;
    print $line;
}
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