use Selective dynamics. for this the POSCAR have to be in fractional coordinates. By adding T of F flag after the coordinates.  and of course ISIF = 2.

POSCAR:

1

a 0 0

0 a 0

0 0 a

X Y

1 1

Selective dynamics

Direct

0 0 0 T T T       # (x,y,z free to move)

1/2 1/2 1/2  T T F #(only x,y free to move)

Thanks for responding Drahomir,

As I mentioned in my post I am aware of flags, my question is how your assuming the freezed coordinates are exactly corresponds to the particular atoms that needs to freeze in the that sturcture.

Thanks

for visualization check this one: http://jp-minerals.org/vesta/en/ . It loads POSCAR file and atom list represents the order in POSCAR. Hope this is what you are looking for.

Use selective dynamics and set the T Flag to F 

Thank you, Aakanksha !