The car was blue.
It was green rather than blue.
Can I say instead of the second sentence:
It was green rather.
and drop the "than blue".
The short answer is no. The word rather cannot normally stand alone. It has to have its friend than along to help it. And even then that is not enough. For example, with the "sentence" It was green rather the reader knows that the sentence is supposed to say that it was green rather than something else, but the something else is not there. The thought is incomplete.