better yet, quote each string argument:

system 'perl', '-pi', '-e', 's/>//g', $filename;
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See? I didn't quote $filename because the variable is already the argument I want to pass to 'perl'.
But you can even do better: instead of calling another instance of perl, do the job right here:

CHANGE_FILE: {
  my $backup = "${filename}~";
  rename $filename, $backup;
  open my $b, '<', $backup;
  open my $f, '>', $filename;
  select $filename;
  s/>//g, print while <$backup>
}
[download]