"Today security forces have moved into the town of Makeen, which is considered as the base headquarters of terrorists," the military said in a statement.
A large part of the town had been cleared and the home of slain Taliban chief Baitullah Mehsud had been demolished.
Twenty-four militants were killed and another was captured in fighting over the past 24 hours, the military said. A total of 21 militants were gunned down around Makeen.
The military's claim came hours after two motorcycle- borne gunmen shot and wounded Brig Suhail and his driver shortly after he left his home in Sector I-8/4 of Islamabad.
Sources said the brigadier worked for the Inter-Services Intelligence agency though there was no word on the incident from the army.
Superintendent of Police Fakhar Alam said the gunmen fled after the attack and police had found some empty bullet casings and a pistol at the site.
Doctors at the Pakistan Institute of Medical Sciences said the brigadier and his driver were in a "stable condition".
This was the third such attack on army officers in Islamabad in little more than a fortnight. On October 22, a brigadier and his driver were killed by militants.
Five days later, a brigadier heading the Defence Services Guards at the army’s headquarters had a narrow escape when his car was ambushed by gunmen outside his home.
The Taliban have vowed to carry out attacks across Pakistan as long as the army continues its operation against them in South Waziristan. The military has mobilised over 30,000 troops for Operation Rah-e-Nijat (Path to Salvation), which is aimed at flushing out an estimated 10,000 Taliban and foreign fighters.
The military said troops advancing from Razmak in North Waziristan entered Makeen on Friday.
Soldiers were conducting search and clearance operations after clearing a large part of the town. "Intense engagements are taking place and terrorists are fleeing, leaving behind their weapons and ammunition," the military said.
Soldiers were consolidating their positions around Sararogha, a former Taliban stronghold. The Taliban targeted troops in the area with rockets and three militants were killed in a retaliatory strike.
Troops also strengthened their positions in and around Ladha, another militant stronghold, and conducted search and clearance operations.
The military says over 420 militants and about 36 soldiers have died so far in fighting in South Waziristan though the figures cannot be independently verified as journalists have no access to the conflict zone.
Security forces also continued search and clearance operations in the northwestern Swat valley, where two militants and a burqa-clad woman carrying a machine gun were arrested. Three militants also surrendered to security forces in this region.
