A character is normally considered flat-footed until he acts in combat (which means no dex to AC, and cannot make AoO's).
So, technically, the target is flat-footed against your attack in the surprise round, and if you win initiative, also in round 1.
However -- You can't make a full attack in a surprise round, since a full attack is a full-round action, and you can only do a move or standard (or charge) in a surprise round.
And yes, uncanny dodge makes it so that you cannot be caught flat-footed - not even in a surprise round by an invisible attacker.
Flat footed ends when the combatant's first turn begins.
Uncanny dodge allows you to keep your dex bonus when flat footed, if I recall correctly.
When does flat-footedness end in the surprise round?
Flat-Footed: "At the start of a battle, before you have had a chance to act (specifically, before your first regular turn in the initiative order), you are flat-footed. You can't use your Dexterity bonus to AC (if any) while flat-footed. Barbarians and rogues of high enough level have the uncanny dodge extraordinary ability, which means that they cannot be caught flat-footed. Characters with uncanny dodge retain their Dexterity bonus to their AC and can make attacks of opportunity before they have acted in the first round of combat. A flat-footed character can't make attacks of opportunity, unless he has the Combat Reflexes feat."
When the opponent gets aware of me or when he acts?
The Surprise Round: "If some but not all of the combatants are aware of their opponents, a surprise round happens before regular rounds begin. In initiative order (highest to lowest), combatants who started the battle aware of their opponents each take a standard or move action during the surprise round. You can also take free actions during the surprise round. If no one or everyone is surprised, no surprise round occurs."
Does Uncanny Dodge make you immune to surprise round flat-footedness?
(Rogue) Uncanny Dodge (Ex): "Starting at 4th level, a rogue can react to danger before her senses would normally allow her to do so. She cannot be caught flat-footed, nor does she lose her Dex bonus to AC if the attacker is invisible. She still loses her Dexterity bonus to AC if immobilized. A rogue with this ability can still lose her Dexterity bonus to AC if an opponent successfully uses the feint action (see Combat) against her."
Why not?
Ah, missed that they have uncanny dodge--for some reason I always look at the feats section for that even though it obviously isn't one.