She can't make any contribution to a *Roth* IRA when filing separately.
She can contribute up to $5500 per year to a *traditional* IRA **if you are not covered** by a retirement plan at your job.
Withdrawing the unqualified contributions to the Roth is not the same as withdrawing money to spend. It is not subject to the 20% early withdrawal (before retirement) penalty. But, while the point of a Roth IRA is that the earnings are tax free, if you withdraw the non-qualified contributions and earnings, those earnings are taxable. If you decide to withdraw the non-qualified contributions and earnings, make sure you tell the IRA trustee that is what you want to do, so they don't code it wrong on your statement.
If she withdraws the non-qualified contributions and earnings from the Roth IRA, she could contribute up to $5500 of that money into a traditional IRA, if you are not covered by a retirement plan at your work.
