It sounds like lichen, which won't hurt the tree, but my concerns are a) that you are keeping the tree indoors, and b) you're watering way too often for a juniper in winter (let more of it get dry in between times). It should be outdoors where you live, though if the pot's small it can be put into a larger one with mulch in between, and don't water if the soil freezes, but it's ok to get snowed on.

Well im keeping the tree in and inclosed porch without heat, and good air circulation. My tree is only in there for winter protection, but seeing the weather situation we have been having im moving the tree outdoors soon, and I will only water the tree once a week. Will this get rid of the lichen?

No, the lichen will grow there if conditions are right for it - but if you don't want it, use some diluted bleach on a toothbrush to scrub it off. Don't ever water anything to a schedule - you must learn to do it when the plant needs it and no more or less. Once a week may be not enough, and it may be way too often. The soil may be mostly peat so may not drain well at all, and may need to be remixed with a lot of grit and bark, and/or the light might have something to do with it, or the time of year.