so basically it is similiar in nature to a plain old copy.

use Unicode::String;
$o_in   = 'in.txt';
$o_out  = 'out.txt';

# get the input data into utf16 objects
open ( F, $o_in ) || die;
while (<F>) {
       push ( @raw, utf16($_));
}
close (F) || die;
# get a list of hex values for the data
map { push (@hexout, $_->hex) } @raw; 
# now create an empty utf16 object 
Unicode::String->stringify_as( 'utf16' );
my $outo = Unicode::String->new();
# and define its hex values
$outo->hex ( join '', @hexout);
# dump the hex values
open ( F, ">$o_out" ) || die;
print F $outo;    
close (F) || die;
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But my input file differs from my output file.

Does anyone have any idea why?

Thanks in advance