Pakistani officials realize that the next phase in Bajaur – the introduction of government and infrastructure – is crucial.
"If the ownership of the people is there and if your presence is there, if there is confidence in the government, we feel there is no reason for them [the insurgents] to return," Major-General Tariq Khan, the Pakistan regional commander who led the operation, told reporters.
"A substantial amount of them have been killed, but that is just an estimate. Nobody can give you an factual figure of how many people are running up and down. They can't even find Osama bin Laden yet," Khan said.
Shaik agrees that al Qaeda's strength in the region remains impossible to gauge.
"How many are leaving and taking refuge in Yemen and Somalia is difficult to tell," she said.
The Pakistani military said that as many as 75 foreign fighters were killed in the final phases of this offensive including Arabs, Chechens, Uzbeks and Afghans.
The military acknowledged that many more may have fled over the border into Afghanistan or elsewhere in Pakistan.
"I would give you a rough estimate that about 25 percent must have gone across the border. Another about 10 or 15 percent might have melted back into the areas of Swat (Valley) etc., where they'd come from," Khan said.
It is also no coincidence that this new vigor in Operation Sherdil comes at the same time as a policy shift in Afghanistan, Shaikh points out.
Officials in Kabul are now prepared to negotiate with the Taliban, and Pakistan is keen to have a say in these negotiations she said.