It is kind of a culture shock between France and the US:

- French visiting the US: why is the waiter coming at us, does he want us out?

- American visiting France: what is the waiter waiting for, didn't he notice we are finished?

If France, if the waiter comes after you have finished your meal and asks you if you are done, it is usually a polite way of asking you to leave, usually because the restaurant is about to close. You are supposed to call the waiter when you are done, or, more commonly in casual restaurants, go pay at the cash register.