I believe that this might be quite a common issue among other FreeNAS users. I have in my network both Mac and Windows PCs and after I mount a share in OS X, multiple folders are created, namely “Network Trash Folder” and “Temporary Items”.
After trying to ignore them for quite a long time I decided to take a deeper look into this. The Oreilly’s Samba Book, Chapter 5, section 2 details some options that can be used here.
The Ubuntu forums also mention this solution which ended up being simpler than I could have expected. I just added the following line to CIFS Settings on my FreeNAS box:
hide files = /Network Trash Folder/Temporary Items/