Aurum,
Sorry to hear about the pinworms. You've got great advice from Bogertophis and it sounds like your vet is on top of it too.
I would make sure the treatment last for a few doses if every 2 weeks. Did I understand that right? The dose is administered every 2-3 weeks? Bogertophis pointed out you want to kill the pinworms and their eggs. So if 2 doses kills all the pinworms, the third dose would presumably ensure that the eggs are dead too. Not an expert, but have dealt with parasites in newly acquired animals before. You want to give medication until all worms and eggs are dead.
Once the treatment is done I would clean the heck out of her tank. Anything plastic - hides, etc. need to be cleaned with F10SC and/or Chlorhexidine solution. Anything that is that is not totally smooth - throw out!
Fake or real branches, rough style hides, vines, etc. All gone. If you absolutely are set on these items, I would soak them in F10SC solution for a while - like days, then rinse with water, let dry and then put back.
However, I would recommend new furnishings.
I would also plan to keep your snake on printless newspaper or paper towels for a while so you can spot any unusual waste easily. I would note that it might not get back to normal right away after medication even if the pinworms are gone.
Finally, I would be changing your water frequently. If you normally change and clean your bowl weekly, do it every 3 days instead. Make sure your snake is staying hydrated with clean water.
Good luck and keep us posted on the progress.
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