Are medicine pills 100% pure or are there some impurities in it since it is hard for me to imagine a process of 100% output or isolation. (And if there are impurities, how do pharmacists know that they won't cause any sort of side effects?)
Contrary to popular belief, most medications are not pure medicine, but do contain other ingredients called fillers. You can see it on OTC medication labels, there are "inert" ingredients which sometimes serve no purpose, or control how the medicine (the active ingredient) is released. This is seen in 12 hour or extended release medications. The medications have fillers that slow the dissolution of the active ingredient, maintaining relief.
Pharmaceutical companies, not pharmacists, actually produce the medications and add the fillers. They are closely monitored by the FDA, to verify that neither the drug nor the fillers have particularly adverse side effects. Every filler must be tested under multiple conditions to ensure that it will have no adverse effects, nor interfere with the performance of the drug.
Usually the term "impurities" refers to a material that is neither medicine, nor filler. This material is not supposed to be in the medication, and consequently may not have been tested for side effects or interference. This is why you should never use online pharmacies. Frequently these medications are pirated formulations that may have fillers not verified by the FDA (which is why they're so cheap), or may have been manufactured under conditions where they were contaminated by impurities.