Not all 100 pins of ATMega 2560 are used in arduino mega

RAJg:
hello everyone i recently saw that there are 16 pins still left in the atmega 2560 ic which has no connection to arduino board ,is there some way that i can utilize that 16 I/O pins in my project.
the unused pin no of ATMEGA 2560 which is 100 pin ic are:
1)pin no 4(PE2)
2)pin no 8(PE6)
3)pin no 9(PE7)
4)pin no 14(PH2)
5)pin no 27(PG2)
6)pin no 28(PG3)
7)pin no 29(PG4)
8)pin no 47(PD4)
9)pin no 48(PD5)
10)pin no 49(PD6)
11)pin no 65(PJ2)
12)pin no 66(PJ3)
13)pin no 67(PJ4)
14)pin no 68(PJ5)
15)pin no 69(PJ6)
16)pin no 79(PJ7)

Hello All! this is exactly what i need, i have made a custum PCB and connect some inverter pins from 74HC04 to pin no 14 (PH2) and Pin no 27 (PG2) does are not connected in the mega 2560 but how can i define (pinMode) does pins as digital input? because on my board i have connected does pins to the Hex inverters..
also PJ4,5,6 and 7 i connected to some IC's and does i neet to define (pinMode) as output