A customer came in and made a large cash deposit into a beneficial trust. We created a section for the transactor and are now creating a section for the beneficial trust. My question is who do I create the CTR as the benefactor. Would it be the trust or do i also have to create sections for the beneficiaries of the trust?

There is no where on a CTR to "create the CTR as the benefactor".

You have the following options:

A Person conducting transaction on own behalf
B Person conducting transaction for another
C Person on whose behalf transaction is conducted

I apologize, my terminology was off. Since the transaction was done on behalf of the beneficial trust how will this need to be added. Will I need to create an entry for each person named on the trust or simply the trust as the person on whose behalf transaction is conducted.

The trust is a separate entity.

If you think the trust is a sham, then I would be looking at filing a SAR. Large cash deposits into a trust account should have a pretty good explanation.

What's a "beneficial trust?"