When re-potting a juniper bonsai tree you're going to have to go through the following procedures. First get it out of the existing pot and then rake out the soil at it's base. After doing so for a while, blast the soil with a water jet. If by chance you encounter stubs of ground level branches, try to remove it with a cutter, otherwise use a pruning saw. Now go back to cleaning and reducing the root mass, having done so as much as possible move the tree into another container. Start backfilling the pot so as not leave any air pockets for bugs and pests to get in from and cause damage to the tree. Now take off all the excess growth to ensure the health of the tree.