The following is an exert from the The Far Orbit Project a Pirates & Privateers Supplement found on page 30 of the referenced book. I have
modified the document to fit my playing style and my views.  These are the rules I use and they have played well.

Raiders (and military vessels) occasionally have to use full power energy weapons against a target eight the goal of disabling the vessel or a specific piece of equipment. (They must know the location of the equipment, i.e.. If your are trying to disable the tractor beams of a Star Destroyer you must know were they are. This knowledge is left up to the discretion of the game master). These rules are used especially if the ship lacks ion cannons.  Note, ion cannons cause the same damage no matter where they hit, they cannot disable 1 component of a ship, its all or nothing. This is quite dangerous with full power energy weapons, since they might accidentally  destroy the prize.  To avoid this, gunners may choose to "call a shot" -target a particular location on a ship.  This is harder than just hammering away at the enemy ship.  Also, a higher scale weapon cannot target a location on a lower scale target - for example, a capital scale ship can target another capital ships engines, but not a starfighters engines.  In the same way, a star fighter can target another starfighters engines or a capital ship's bridge, but not a walkers legs, or head.

Targeting a primary section of a ship (the shield generators of a Star Destroyer, the engines, the landing bay, the main body) adds +2D to the difficulty to hit. Targeting a sub-section of a ship (a gun battery, a particular engine, the shield generators, the command section,) adds +4D to the difficulty to hit.  Targeting a specific location of a ship (a specific gun, the bridge, a maneuvering thruster, an engines thermal exhaust port) adds +8D to the difficulty to hit. Note remember to compensate for scale differences, for example, if a X-wing is targeting a maneuvering thruster of a Star Destroyers it would only add a +2D to the difficulty to  hit [ +8D for specific location, -6D for scale difference =+2D].
 

Location: Modifiers:
Primary section +2D
Sub-section +4D
Specific location +8D
Damage should be worked out normally, remember this could still destroy the the target.  The specific results should be determinedly the game master using the normal starship damage results guidelines.

In general, a lightly damaged location loses -1D or -1 move, a heavily damaged location loses -2D or -2 move, a severely damaged location is disabled and unable to perform its function, and a destroyed result indicates that the location has suffered catastrophic damage (this may mean that the engines have overloaded, or that a gun explodes, setting off a chain retain of gun explosions).  Targeting locations doesn't guarantee that a ship will be simply disabled, but it does increase the odds of capturing a ship with minimal damage.
 

Damage: Penalty:
Light damage -1D or -1 move
Heavy damage -2D or -2 move
Severe damage system disabled
Destroyed Catastrophic damage:
threatens ship