They can be difficult.
One reason is that cherry get blossom blight sometimes, which kills twigs or portons of twigs.
Basically, I prune the limbs away from under and inside, and let the
tree build up on itself, trying to leave as much of the top, and removing only from the interior.
Certainly, dead stuff comes out.
I always raise the canopy a bit off the ground, like 3' for a small
tree like a 10 footer, or 5' up for a 20 foot tall
tree.
That allows air circulation which helps to reduce the fungal problems a bit.
