Well, yes. But it will require effort.
The easy way would be to use Selective Spell. The caster would be able to select casting stat mod 'targets' to avoid. With spells that just target an area (like Darkness) it would mean you could exclude that many squares.
Yes, strange as it may seem you need to raise the level of the spell to control the area a little. There use to be feats in 3.5 that let you change the shape of an area of effect, but those didn't make it into Pathfinder.
The second option would be to research a version of the same spell with a smaller area of effect. Generally speaking the spell would retain the same casting level unless it was a dramatic difference in effectiveness. This would require time and gold to accomplish.