foreach $files (@ARGV) {
...
    foreach $line (@lines) {

        #Mapping des charges directes
        seek MAPPINGFILE1, 0, 0;
        while (<MAPPINGFILE1>) {
...
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Mentioned, but here to be clear. Nothing you do is going to help if you're nesting loops. Also, checkout this talk on Supercharging Perl from YAPC this year.