Are you talking about income taxes? If so you can pay the taxes due. The issue you might have is that it takes a few weeks for your tax transcripts to show up at the IRS which will be pulled by the lender.
Feel Free to contact me for more details.
Shane Levine- Loan Officer
United American Mortgage
Are the outstanding taxes currently a lien listed on your credit? If so you will have to pay those before getting a conventional loan. A hard money lender may lender to you with a very large down payment.