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`sed 's/^ \{2,\}//' -i filename.html`;

system('sed','s/^ \{2,\}//', '-i', 'filename.html') == 0
    or die "Couldn't launch sed: $! / $?";

use Tie::File;
my $filename = 'filename.html';
...
for (@file) {
    s/^ {2}//;
};