Pap smears are not designed to detect warts or herpes. Your negative results don't prove or disprove that you don't have HPV, warts, or herpes.
Clarify with your doctor whether or not she made a definite diagnosis of warts. That diagnosis is based on
visualVisual acuity test inspection, not a lab test. If so, fill the
Aldara prescription and use it as directed. If not, or if she wasn't sure, using Aldara might just confuse things: If the bumps persist, they could still be warts (because Aldara works only 60-70% of the time); and if they go away, they might not be warts.
If your doctor is uncertain, consider getting a second opinion, e.g. from your local health department STD clinic or perhaps a family planning clinic like Planned Parenthood. In the meantime, please read up on both herpes and HPV, which have been covered in great detail on this forum. A good starting point is the link "STD Quick Facts and Articles" at the top of the STD Forum home page.
Good luck-- HHH, MD