# Set the input and output filenames
my $ifilename = 'file.in';
my $ofilename = $ifilename . '.bin';

# Open the files and ensure we handle them as binary data
open my $ifile, '<', $ifilename or die "could not open input file $!";
open my $ofile, '>', $ofilename or die "could not open output file $!";
binmode $ifile;
binmode $ofile;

# Read the binary data
$_ = do { local $/; <$ifile> };

# Replace the initial bytes with zero
s/^(.*?)(\x4F\xFF)/"\x0" x length($1) . $2/se;

# Store the result in the output file
print $ofile $_;

# Tidy up
close $ifile;
close $ofile;