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There is a search feature but it only searches in the title or the author.
What you want is to use the My Files section of the Nook which allows you to use a directory structure. You could use the Shelves option but the Nook has a nasty habit of removing any sideloaded books (ie books you added yourself and didn't buy from B&N) from the shelves if you don't disconnect properly from your computer.
To find the My Files on your Nook when you're in Library mode just underneath LIBRARY you'll see a box that probably says BOOKS or ALL. Touch that and then select My Files. Then select NOOK Files or Memory Card on the right hand side of the screen if you have a memory card.
The best way to take advantage of this using Calibre is to use Custom Columns and a customized template in the Send To Device section of Preferences. I have three custom columns - Library, Genre1 and Genre2. The Library column is because I have a Non-Fiction library, a Fiction library, and a Fanfiction library. Genre1 is for main genres such as Science Fiction, Fantasy, History, or a Fandom ie Harry Potter. Genre2 is for more specialized genres such as Space Opera, Urban Fantasy, Military - Civil War, Alternate Universe, etc. In Preferences|Sending Books to Device|Save Template I put the following: {#library}/{#genre1}/{#genre2}/{series}/{series_index:>2} - {title} - {author} This template will give me the following results:
Fiction/Science Fiction/Dragons/Pern/01 - Dragonsdawn - Anne McCaffrey
Non-Fiction/Biography/Military/SEAL Team Six - Howard E. Wasdin
Fanfiction/Harry Potter/AU/Raising Harry/01 - Living La Vida Muggle - Aramie.Greyson
Using this method makes it very easy to sort thru my books to find what I'm looking for and is much better than the Shelves method because I can have as many sub-directories as I want whereas the Shelves are all single level.
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