I am a young man who is in the habit of checking his garment to make sure they are pure. When I find stains, I am not sure whether they are drops of urine or other stains. At one point I decided to see a physician, however, after making Istikharah, I did not go, but I am still worried. Is it permissible for me to make Istikharah if I doubt my purity? Please answer me, may Allah reward you with good!

Praying Istikharah is always a good thing. Yet, Istikharah is offered regarding permissible matters and not obligatory, desirable, prohibited or undesirable matters. Obligatory and desirable matters are done without offering Istikharah, just as undesirable and prohibited matters are avoided without offering Istikharah.
As for the inquirer, he seems to be always in doubt and he needs to ignore these ideas. He may follow the opinion of Imam Malik (may Allah be pleased with him) who says that sprinkling the garment with water eliminates the effect of any stains of urine. All you have to do is to sprinkle your garment with water. This view is adopted by Imam Ahmad as well. The basic ruling of objects is that they are pure. Thus, the garment is pure unless you are certain it is not.