Your 401k plan is required to split the pre-tax and after-tax funds, and rollover the pre-tax funds to a traditional IRA and the after-tax funds to a Roth IRA. The pro-rata rule does not apply to qualified workplace plans. After the rollover, you will have a Roth IRA and a traditional IRA, and your traditional IRA will not have any portion of after-tax funds (unless it did already for other reasons).
