Well sir, you should just dip the cleaners into ISO alcohol and insert them into the stem and clean as usual. Try not to get the alcohol on the finsih of the pipe or stem. And you can do the same thing with the shank of the pipe just remember not to get any on the exterior and let them dry WELL over night before smoking them. I use tapered cleaners and Q-Tips for the shank, makes it easier to get all the crud out. You can also retort your pipes but, that's a different story and involves boiling alcohol and can be a bit dangerous if you don't know what your doing.
Oh, and this works well with Vulcanite and acrylic/Lucite stems
One other note, the higher the percent of the ISO the better cleaning abilities it has, I use 90%. Although you can use Everclear or any high proof alcohol.