A method and apparatus performs processing of the non-access stratus (NAS) layer (layer 3) in long term evolution (LTE) wireless transmit/receive units (WTRUs), which allows the NAS protocol layer to route layer 3 messages to the correct NAS entity, and to encode new NAS message types and information elements. A new architecture is presented that enables NAS security. When a NAS message is generated, a determination is made as to whether or not to cipher, de-cipher and/or integrity check the NAS message based on at least one of a protocol discriminator (PD) of the NAS message, an indicator field in a header of the NAS message, the type of the NAS message, a NAS security state variable, and an indication by an upper layer protocol. The NAS security state variable indicates whether NAS security is currently active or not and may comprise one bit.