Do you have any idea how many people work for the US government? The State department alone has 12K civil service employees (not counting many more than that out in the field), the DOJ has well over 100K employees... and there are many more departments.
You can't just fire everyone day one and expect the country to still function... you have to take a top down approach to get proper leadership reestablished and work from there. Further complicating things is the reality that all the top positions have to get confirmed by the Senate.
Obama had 8 years to fully corrupt the place... and the place already had decades of rot in it when he started.
Its going to take some time to drain that swamp.
The swamp draining will be in phases and we're still early in Phase I. We've waited decades, we can have the patience to see this done properly.