When your financial institution is opening new accounts for business entities, you may want to have the entity complete a commercial account checklist that asks various questions that will help you conduct your risk assessment including determining if a new customer is an MSB.
As for your current customers, if you suspect they are an MSB in accordance with the definition of an MSB (31 CFR 103.11 (uu)), I would have the person responsible for the account (branch manager) contact or visit the customer and ask a few questions. If it appears they would be classified as an MSB, require them to present the materials as stated in the Interagency guidance. Additionally, if they are classified as an MSB and they are not registered, you will need to file a SAR on them.
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The opinion stated here is what it is, My Opinion.