Quintus Curtius has a fine article on his web site about Pompey’s most impressive victory:

Every victory seems easy in retrospect, of course.  But the campaign against the pirates was successful for very specific reasons.  They are as follows:  (1) deployment of sufficient forces to deal with the threat; (2) assignment of specific sectors of operation to local commanders, with each one made responsible for what happened in his area; (3) relentless pursuit of fleeing pirates so that they could not rest or hide; (4) a policy of “paroling” captured pirates and allowing them to return to their homes provided that they swore to abandon crime; (5) execution of the worst offenders; and (6) the capture of the main pirate strongholds in Cilicia.

These principles translate well to the modern age:

• Overwhelming Force – The insurgent must respect your strength, and eventually learn to fear attacking you.
• Divide, Clear, and Hold – pick the areas where they are weakest. Secure these first. Then painstakingly expand into areas where they are stronger, and drive them out of these. Pompey didn’t try to do it all at once; he ground them slowly down. This is the only thing that has ever worked.
• Mercy to the Masses, Punishment to the Criminals – As Sun Tzu reminds us, men with no possibility of escape will fight to the death. The impulse to treat all insurgents the same must be avoided. During the Chinese Civil War, the Communists made it a policy to release Nationalist enlisted men who surrendered, and only imprison or kill their officers. This made it hard for the Nationalists armies to maintain fighting morale. The United States Army used a similar policy to great effect against Aguinaldo and the Phillipine insurgents at the turn of the 20th century. Any rebel could surrender and be paroled; only those accused of specific crimes would be punished.
• Co-ordination. The disadvantage of government forces is that they lack the complete freedom of movement the guerrilla has, being weight down by the need to defend territory and the weight of institutional impedimenta. But with shared responsibility and independent action, they can bring their strength to bear.
• Attack Their Sanctuary. None of the above matters if the insurgents can constantly regroup safely. Successful insurgents almost always have safe areas where their enemies cannot or will not go (North Vietnam and Cambodia, Tribal Areas of Pakistan, etc.). All effort must be made not to allow this.  When insurgents have no sanctuary, and their supplies are cut off, their institutional weaknesses become fatal.