If you want to copy Word files manually, you'll have to remember that these are binary files. Thus,
Use binmode on your filehandles to ensure that Windows won't break the document by "fixing" newline symbols.
Newlines in binary documents don't usually represent newlines in their contents, so it may be useful to use read, not readline (which is the synonym for <>).
Don't modify data you're copying in any ways unless you know what you're doing ("$_\n" is not a good thing in case of binary files).