It says it all in the title, if cree leds datasheet says 3-3.6V what do I calculate if want to design serial leds, 3.3V? Or they use whats available? It can be used with 9V supply without resistor or with 12V supply with some resistors?
All LEDs are "current controlled" devices. Their voltage is variable based on heat, age, individual differences, etc. If the Cree datasheet says 3-3.6, then each one may be 3, or 3.6, or anywhere in between, those are the outer limits (any produced outside that range are discarded or not sold as the standard product).
So bottom line, you simply can't do what you are talking about, without at a minimum testing, and realistically, you need a constant-current supply. (Many Cree LEDs are at, or below, the lower limit of their specs).
Having said all that, if you run 3x LEDs in series (nominally 9+ volts) and you are talking about a 9V alkaline battery, you have nothing at all to fear, a 9V battery cannot put enough power out to destroy 3 power LEDs, they can't generate the needed current, even if the shelf voltage is above 9V, it'll fall instanly below the safe LED levels when connected.
If you are talking a 9V, or 12V, wall-power transformer, you'll likely blow the LEDs, possibly even with the 9V, as the instantaneous connected current of most 9V transformers is WAY higher at initial connection. An LED can blow in nanoseconds, if the 9V wall-transformer is floating at 16V "open circuit", and connected, it'll dump way too much current into the LEDs. They MIGHT survive, they might not.
Bottom line, you really need some form of constant current regulator, or need to know for sure exactly what your power source is going to do, test the LEDs in series at their operational voltage to match desired current, then at the minimum pick a resistance that matches all that.