If I open files I created in Windows, the lines all end with
dos2unix is a commandline utility that will do this, or
:%s/^M//g will if you use Ctrl-v Ctrl-m to input the ^M, or you can
:set ff=unix and vim will do it for you.
Alternately, if you move files back and forth a lot, you might not want to convert them, but rather to do
:set ff=dos, so vim will know it's a DOS file and use DOS conventions for line endings.