Heres a technique that I mostly used in the modeling to fix or shaping a highly dense mesh.
(see the 2nd attachment for a better explanation)
Notice it gives a much cleaner results instead pulling the vertices manually one by one.
You can set the FFD as a shortcut, which I mostly uses are the 2x2x2 or 3x3x3 or custom (box)
Hopes this technique found useful for people in the modeling, and if you have any suggestions
or a request, feel free to ask.
–click to enlarge–
Siregar3D 
Interesting and helpful!