Is total cover determined by ability to target a creature's "square" or their body?

[Talakeal]

For example, a medium creature (occupying a five foot square) is crouched behind a 3 foot high wall. I can easily target the creature's square, which is 5' high, but I can't see the actual creatures body. Does the creature have Total Cover or just regular Cover?

[Slipperychicken]

[determining if he has normal cover]

He has cover if a line between your square and his goes through a wall. This appears to be the case, so he gets cover.


Cover
To determine whether your target has cover from your ranged attack, choose a corner of your square. If any line from this corner to any corner of the target’s square passes through a square or border that blocks line of effect or provides cover, or through a square occupied by a creature, the target has cover (+4 to AC).

When making a melee attack against an adjacent target, your target has cover if any line from your square to the target’s square goes through a wall (including a low wall). When making a melee attack against a target that isn’t adjacent to you (such as with a reach weapon), use the rules for determining cover from ranged attacks.

Low Obstacles and Cover
A low obstacle (such as a wall no higher than half your height) provides cover, but only to creatures within 30 feet (6 squares) of it. The attacker can ignore the cover if he’s closer to the obstacle than his target.

EDIT: Considering the portion of his body which is obscured it may even qualify as improved cover (as described in the "Varying Degrees of Cover" section), from which he would gain double the normal AC and Reflex save bonuses from cover.

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Now to determine whether the target has total cover. Let's see...


Total Cover
If you don’t have line of effect to your target he is considered to have total cover from you. You can’t make an attack against a target that has total cover.


So line of effect would have to be blocked for there to be total cover.


Line of Effect
A line of effect is a straight, unblocked path that indicates what a spell can affect. A line of effect is canceled by a solid barrier. It’s like line of sight for ranged weapons, except that it’s not blocked by fog, darkness, and other factors that limit normal sight.

You must have a clear line of effect to any target that you cast a spell on or to any space in which you wish to create an effect. You must have a clear line of effect to the point of origin of any spell you cast.

A burst, cone, cylinder, or emanation spell affects only an area, creatures, or objects to which it has line of effect from its origin (a spherical burst’s center point, a cone-shaped burst’s starting point, a cylinder’s circle, or an emanation’s point of origin).

An otherwise solid barrier with a hole of at least 1 square foot through it does not block a spell’s line of effect. Such an opening means that the 5-foot length of wall containing the hole is no longer considered a barrier for purposes of a spell’s line of effect.

Using RAI, as long as you have at least a 1ft hole to see the creature, you have line of effect. Since the creature is entirely obscured by a wall, that wall blocks line of effect and grants the creature Total Cover.