SR4A p. 185
When a protected character is targeted with a spell, she rolls Counterspelling dice in addition to the appropriate attribute (Body or Willpower) for the resistance test.
So technically one could argue that Spell Defense doesn't work against location targeted indirect aoe-spells. On the other hand we have a resistance test mentioned, which would be the next step after launching the spell.
So while Spell Defense would not be able to do anything against the casting, it would aid in diminishing the effect of the spell by giving more dice to resist its damage.