-d pathname will test if pathname exists and is a directory. If you want more resolution, you can say

if (-d $pathname) {
  # $pathname exists and is a directory
  # ...
}
elsif (-e _) {
  # $pathname exists, but is NOT a directory
  # ...
}
else {
  # $pathname doesn't even exist
  # ...
}
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Note the use of the special pseudo-filehandle _: it's used to test the last filehandle tested. See perlfunc for more details of this.

In any case, testing for existence of a file or a directory is often indicative of a bug. It is almost always better to try to get what you need in a single operation. For instance, instead of saying

if (-d $d) {
  open FILE, "$d/$f" or die "Open failed";
}
else {
  die "No directory $d";
}
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do just the open:

open FILE, "$d/$f" or die "Open failed";
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Let the operating system make sure your path is OK. The first way is subject to an insiduous race condition: directory $d could be created between the test -d $d and the error message, and the error message would be wrong. This is not too bad; but if some more complex error handling were used, it would be likely to break.

So try not to test if you can do something with -X; just try to do it. If you can't, the OS will let you know.