Hope you're not using plastic baby bottles. Plastics can react with acidic foods/juices, high heat, chlorine and possibly even your baby's meds.
If you're using glass baby bottles, suggest you look up your baby's med. Knowing the chemical composition of the med can sometimes help you figure out what cleansing method might work best.
[url="http://www.nlm.nih.gov/medlineplus/druginfo/medmaster/a685002.html"]http://www.nlm.nih.gov/medlineplus/druginfo/medmaster/a685002.html[/url]
Or call, email or visit the drug manufacturer. Since labs are always washing test tubes, I imagine they would have some suggestions.
There's an excellent post on the Cancer Topics board about plastics and microwaves. Pls read it. Unlike many other microwave stories, this one is not an urban myth.