When I do mine with hand tools I secure the frame to a scrap of 1 x 2 lumber with screws though the frame screw holes at each end. The lumber is also shaped to accept the frames profile to ensure a flat fit to fully support the frame.
I then screw the lumber to the work bench and hacksaw and file away.
This is a VERY good approach. As I'm sure everyone here is aware, you might not actually "break" the frame by leaning on it too hard while shaping it, but you can sure deform it, and even if it's only a little bit, you might never be able to get the motor, bearings, and trucks to go back in and run quite as smoothly if that happens.
