You're using system to execute a shell script which then executes other commands. My suggestion is skipping the shell script altogether, and using system to execute those commands directly from Perl.

For example:

foreach $key (keys %hash) {
  my $cmd = "$program $key $matrix ";
  $cmd .= "$path/CISCO_$_.clean " for @{$hash{$key}};

  system($cmd) == 0   # system returns 0 on success
    or die "system '$cmd' failed: $?";
}
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