\r\n in the file is converted to \n in perl when you open the files in "text" mode so you have to use "binary" mode:

#! perl -w
# Convert a dos format file to Unix removing ^M Char from file

my $FileOpen = $ARGV[ 0 ];
my $FileTemp = "$FileOpen.Temp9687";

open OPEN, '<:raw', $FileOpen or die "\nCan not open file $FileOpen $!
+\n";
open CONV, '>:raw', $FileTemp or die "\nCan not open file $FileTemp $!
+\n";

local ( $/, $\ ) = ( "\r\n", "\n" );

print CONV while <OPEN>;

close OPEN;
close CONV;
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