They are not terribly powerful, but attack in groups and can be a nuisance, since the player is only in command of Celes and Locke. Their special attack, Desperate Strike, sometimes lets them attack twice a turn. An efficient way to kill them is to have Celes group-cast Blizzard on them, weakening them enough for follow-up normal attacks to defeat them. Alternatively, the player can equip Locke with a Gauntlet or Genji Glove, boosting his damage output enough to defeat them in one hit without the need for Celes' magic.
Strangely enough, Commanders can still be encountered and fought in the South Figaro basement after the end of the world, even though the Empire has been wiped out, and the soldier at the Dragon's Neck Coliseum claims to be the last Imperial soldier left in the world.