From the Sperry Home Garden

One of the challenges in pruning junipers is that they are reluctant to send out new branches if you cut away all of the existing ones. Therefore, when you prune a plant like this Sea Green juniper you have to use lopping shears and you must reach into the center of the plant to clip at the juncture of one of the smaller branches.

Your goal, when you have finished pruning your juniper, should be to have removed all the branches you need to without leaving any visible stubs. The cuts will all be of different lengths so that the plant will still have its natural form when you’re through. You can see the results here.