Is it  possible to create a folder in iBooks? I have iPad and iPod touch. Both I bought just for reading books in pdf format.

If it is possible, I want to create some folders to separate the books based on categories I will define.
Yes, as long as you're running the latest version.


Tap the button a the top of the bookshelf where it likely says "Books" (though it might say "PDFs") -- this is the Collections button.
Tap "New" to add a new collections folder with a name of your choice.
Tap the "Books" collection and you'll see all of your books. 
Tap the "Select" button in the upper-right corner, then tap on all of the books you want to move into a collection.
Tap "Move" and select the collection you want to move the books into. 


Poof, they're now out of the default "Books" collection and now in the collection you chose.