No, it is not necessary to fill all the seats reserved for girls. As there might be a case where the no. of seats reserved for girls (in a particular IIT) is more than the no, of girls candidate applying for that particular IIT.

The reserved seats which are not taken by girls remain vacant for that session and no boy is allowed to take admission on that particular reserved seat. However, if the no. of girls is more than the no. of reserved seats then on the basis of their ranks, they might get admission on an open seat (un-reserved seat).

Hope it helps.