You are posting different code to what you are running. You know perl is case sensitive? Anyway  next if $File =~ m/^\./ *will* skip* the . and .. dirs. It is better written (more spcific) as next if $File eq '.' or $File eq '..' but it will work. It will skip anything with a leading dot but that is rare on win32 as although you can use it it does not hide the files.

C:\tmp>type test.pl
#!/usr/bin/perl -w
opendir D, '.' or die $!;
while( $file = readdir(D) ) {
    next if $file =~ m/^\./;
    print "Got $file\n";
}

C:\tmp>test.pl
Got A
Got bookmark.htm
Got inherit.pl
Got temp.dir
Got temp.pag
Got temp0.txt
Got temp1.txt
Got test.pl

C:\tmp>
[download]

No dot dirs present. No warnings. Now comment out the next.....

C:\tmp>type test.pl
#!/usr/bin/perl -w
opendir D, '.' or die $!;
while( $file = readdir(D) ) {
    #next if $file =~ m/^\./;
    print "Got $file\n";
}

C:\tmp>test.pl
Got .
Got ..
Got .foo
Got A
Got bookmark.htm
Got inherit.pl
Got temp.dir
Got temp.pag
Got temp0.txt
Got temp1.txt
Got test.pl

C:\tmp>
[download]