Fire them all.
Recess appoint those who are deemed necessary.
Trump should bypass the Senate using the Obama precedent, create “czars” where he needs agency bosses. They can be utilized for each agency until and unless the Senate gets around to confirming appointments. Else, we are going to go several years with the new bosses trickling through the Senate. The Republicans, being the wholly owned subsidiarians of the Democrat Party will “slow-walk” everything and will shoot down whatever they can get away with.
I’ve suggested shutting down entire departments just to get rid of the vermin. He can always reconstitute them under a different name if they serve legitimate purposes such as State or Justice.