After looking for AT91 and USB 'on the go' specifics with little success, I noticed the USBHost library provided in the IDE download uses a library from circuits@home: GitHub - felis/USB_Host_Shield_2.0: Revision 2.0 of USB Host Library for Arduino.
There is already a mass storage interface there, weather it works or not I do not know ( someone who has used the USB host shield may be able to answer this. )
Editing it shouldn't be too hard if modifications are needed. It will still need a library on top to provide a 'client' interface. The mass storage interface is just implementing a way of sending/receiving commands/data too and from a USB device that supports the MSD protocol, not much in the way of file system control.