I'm at the part of the quest where the NCR wants me to take care of the Brotherhood of Steel but I'm stuck.I've gone to hidden Valley and when I check my local Map it takes me to the holled out rock but I have know idea what I'm supposed to do.

There are multiple bunkers in Hidden Valley. The Brotherhood is holed up in one of them.

I found the bunker and have done there earlier quest's,I need to know how to kill or take care of the Brotherhood for the NCR.

You have to unlock the mainframe and initiate the self destruct sequence. There are three keys held by the leaders. You need them to open the console unless you have 100 lock pick. There is also a console command for the PC you could use to cheat. Stealing these keys is the best way to get them since killing the owners will bring the house down around you.

If McNamara's still the Elder then you can talk to him and negotiate a deal with the Brotherhood and NCR, otherwise you'll have to activate the bunker's self-destruct mechanism (pickpocket the elder, the head scribe and the head paladin for the required keys and have a stealthboy handy for the escape). Or you could try and take them out all-guns blazing...