12 Bit interface is not possible with GPIF. You have to use 16 Bit GPIF. The extra 4 bits need to be removed either in Fx3 or in the host application. If it is done in FX3, the throughput will be afftected. So we recommend to do it in the host application.
Thanks for valuable suggestion.Is there any documents for filtering the extra 4 bits.we are using C# with Cyusb.dll .
When received data, mask 4 bits You don't use.
That's my solution, and it;s working.