Raid the suspected houses, terror hide-outs, etc.
Arrest the suspected terrorists and put them on trial in a court of law.
Drones are inefficient and they kill civilians more than they kill the suspects.
However, civilians would also die in the military campaign that would be waged to secure the area enough to allow police raids and arrests.
The problem isn't that drone attacks are being made in Pakistan. The problem is that another country, not Pakistan is carrying out attacks - that's a violation of sovereignty. I'm all for targetting militants by air - just as long as it's Pakistan doing it and no-one else.