They just use bulldozers to flatten whatever the bombs don't. They can drive a bulldozer pretty precisely, especially when they don't care who's in front of it or under it.
Caterpillar even supplies the IDF with bulldozers just for this purpose, which then get up-armored and sent into Palestinian civilian areas to do this (including unmanned versions).
By the time the bulldozers are there civilians have long moved out of the area.