Just remove them.

my $dir = "/opt/DSPKG";
opendir(my $bin_dh, $dirs)
   or die "Can't open directory $dir: $!\n";

my @subdirs = grep { !/^\.\.?\z/ && -d "$dirs/$_" }
              readdir $bin_dh;

my $pkg_file = '/tmp/pkgtest';
open(my $pkg_fh, '>', $pkg_file)
   or die "cant open pkgtest $pkg_file: $!\n";

foreach my $subdir (@subdirs) {
   print $pkg_fh "$subdir\n";
}
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Other fixes:

• Added omitted file handle in print statement.
• Eliminated the use of global variables (BIN and MYFILE).
• Adjusted the number (singular/plural) of variable names. (For example, $dirs held the name of one directory, so I renamed it to $dir.)
• Tried to use more meaningful names. You'd be able to pick even better ones since you know what this code is doing.
• Used safer 3-arg open.
• Added \n to die messages. The user does not need to know the line number at which the error occured for those errors.