I want to create a driver for the Motorola 68000 in assembly code and the interruption handler must be atomic, how can I do it? (I only want to solve the atomic problem, the ISR already got it)
You can do it by ensuring that no other interrupts can interrupt your handler.
Of course, according to this page, the 68000 has non-maskable interrupts, so there are interrupts which can't be disabled and that will interrupt your handler.
Are you sure you mean that the entire handler must be atomic, though? Usually it's enough if some critical operation is atomic, one that shares state with non-interrupt code.