On any NPC or player that you have scanned completely, you can select subtargets. The settings menu offers hotkeys for this, which are recommended to be used instead of manually selecting them in the left hand panel. Most weapons will automatically aim for the subtarget you have selected, making it easy to apply targeted module damage after enemy shields are down.
Here are the benefits of the more important subtargets in PvE combat:
Power Plant: Destroying the power plant disables shield rebuilding. Inflicting further damage to an already destroyed powerplant has a chance of instantly destroying the ship.
Frame Shift Drive: Destroying the FSD inhibits NPCs from jumping out.
Shield Generator: Destroying the shield generator stops shield rebuilding.
Drives: Destroying thrusters leaves NPCs without thrust capability (they will drift off) and will also prevent them from jumping out. However if they were going fast enough they may be tough for you to catch up to.
Further using a subtarget will make it easier to use hitscan weaponry in dark areas or on far away targets, as it offers a much more precise point to aim for than the target selection brackets.