You can schedule an AFT (Automated Funds Transfer) or CFT (Check Funds Transfer) from an IRA certificate the same way as from an IRA savings account. CU*BASE will perform the scheduled transfer, withhold any scheduled taxes (you can specify either a % or a specific $ amount for Federal and/or State backup withholding on the AFT/CFT setup screen), and will not charge a penalty for certificates. The transfer will take funds from the principal balance of the CD if necessary.
When completing the AFT or CFT setup screens, just be sure to check the "IRA payout distribution" flag and fill in the appropriate Federal and/or State Income Withholding fields as computed for your member's specific situation (refer to IRS guidelines).