Message lengths with AES CTR mode?
Well, lets try to take a concrete example:

Suppose that you have a 142 bit message that you need to encrypt with CTR mode.  What do you do?

Well, you generate the first 128 bit block with AES; you take the first 128 bits of the message, exclusive-or the two, and that's the first 128 bits of the ciphertext.

Then what?  Well, you have 142-128=14 bits of plaintext left.  So, what you do is generate the second 128 bit block with AES; you then take the first 14 bits of that, exclusive-or that with the 14 bits of plaintext, and that gives you the last 14 bits of the ciphertext.  And, what do you do with the remaining 128-14=114 bits of AES output?  Well, you discard it -- you don't need it.

If the decryptor does precisely the same logic, he will transform the 142 bit ciphertext into the original 142 bit plaintext.

Does this make things clearer?