Assuming no pre 1987 after tax contributions, the only sure way to accomplish this is rather ackward and requires some other funds to complete the pre tax rollover due to mandatory withholding.

Since direct rollovers probably trigger the pro rate rules resulting in 90% of the after tax amount going to the TIRA and only 10% to the Roth and making the Roth conversion mostly taxable, the indirect method can take advantage of indirect rollover provisions in the tax code from 2002 which state that an employee rollover is first funded by the pre tax balance. Therefore, if the employee asks for a indirect distribution of the full balance, he will get 100,000 less 20% of 90,000 or 18,000. which goes to the IRS. Employee must come up with the 18,000 to complete the rollover of 90,000 to the TIRA first and after this the 10,000 as a tax free Roth conversion. The 18,000 in withholding is subject to refund upon filing the 2009 return. The TIRA rollover must be done FIRST.

It would be much easier if this could be done by direct rollover, first to the TIRA and then the remaining 10,000 to the Roth. But the IRS has not issued any regulations stating that this can be done, and the pro rate rules may defeat this idea. The indirect method however uses current rules that clearly make the 90,000 rolled over by the employee pre tax dollars. The remaining 10,000 therefore have to be the after tax dollars, and they go to the Roth. For 2009, the 100,000 income limit still applies to qualify for this Roth conversion.

The only release by the IRS to date on direct Roth conversions is Notice 2008-30, and this notice does nothing to clarify the basis segregation issues.

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