anubodh said:
the singularities inside are still separated
No, they aren't. The singularities are not places in space; they are instants of time, which are to the future of all other instants inside the horizon. If two black holes merge, then there is only one singularity, not two, because there is only one "inside the horizon".
This is an area where you have to really train yourself to think in terms of spacetime, not space. A single black hole's horizon is not a 2-sphere; it's a 3-cylinder in spacetime, which you can imagine as a cylinder if you suppress one spatial dimension. The singularity is at the future endpoint of the interior of the cylinder.
When two black holes merge, in spacetime, there is really only one horizon, and always was--it's just shaped like a pair of trousers instead of a cylinder. The region where there are two "legs" of the trousers corresponds to the period of time before the holes merged, and the region where there is just one "trunk" of the trousers corresponds to the period of time after they merge. So there is only one "interior" and therefore only one singularity, at the future endpoint of the trunk of the trousers.
anubodh said:
can we apply external forces in opposite directions so that these singularities start separating.
No, because there is only one singularity. See above.