Yes, the loop around which you are computing the emf must always be the boundary of the surface.
If you are confused about this, I would suggest that you watch
Walter Lewin talk about it (start at 5:00) if you haven't already.
As for an example, basically any Faraday's Law problem will do the trick.
Here's an example: A circuit consisting of a circular loop of wire (radius 1 cm) and an LED is placed inside a solenoid, with the loop of wire concentric with the coils of the solenoid. The solenoid is turned on and the magnetic field inside smoothly increases to 0.1 T over 0.001 seconds. The LED has a 1 ohm resistance and will explode if a current greater than 50 mA flows through it. Does the LED survive?
Answer: We want to calculate the EMF of the circuit, so the circuit has to be the boundary of my surface. I choose the flat surface, which is just a circle, and in this case I am in luck -- the magnetic field is perpendicular to that surface. So the magnetic flux is BA. The rate of change of magnetic flux is 0.1 T * pi(0.01 m)
2/0.001 s = 0.01*pi Tm
2/s. Therefore, the emf is 0.031 V, which produces a current of 31 mA. That is not enough to explode the LED.