In vi use the following:
:%s/^M/\n/g
or with perl on the command line:
$ perl -pi.bak -e 's/^M/\n/g' <filename>
NOTE: Be sure to create the ^M by typing ctrl+V followed by ctrl+M.
^M is ASCII 13 (Ctrl+M), which is the carriage return.
Different operating systems use different symbols to set the end of a line/new line.
Unix uses newline (\n)
Mac uses carriage return (\r)
And Windows/DOS use both (\n\r)
To prevent the ^M from showing up in files, be sure to use ASCII (text) mode when transfering text files.