Here is an example. I'm sure someone will correct me if I'm missing something.
Assuming 908GP32:
1) Wire horizontal matrix wires directly to PTA4, PTA5, PTA6, PTA7
2) Wire vertical matrix wires directly to PTA0/KBD0, PTA1/KBD1, PTA2/KBD2
3) Set PTA4-7 to output and drive them low
DDRA = 0xf0; // PTA0-3 input, PTA4-7 output
PTA &= ~0xf0; // PTA4-7 low
4) Enable pullups on PTA0-2
PTAPUE = 0x07; // PTA0-2 pullups enabled
5) Enable keyboard interrupts on PTA0-2
INTKBIER = 0x07; // PTA0-2 keyboard interrupts enabled
6) Enable interrupts in main()
asm cli;
That's all you should have to do. Now in your keyboard ISR, you do the normal polling where you set PTA4-7 low one at a time and read PTA0-2 until you find which key was pressed.