The multimedia community is moving from monolithic applications to more flexible and scalable proliferate solutions. Security issues such as access control and authentication of multimedia content have been intensively studied in the literature. In particular, stream authentication tends to be more complicated since a stream may be transcoded by intermediate proxies or composed by multiple sources. Traditional stream authentication schemes consider a stream as a group of packets and authenticate these packets over an erasure channel. However, by fixing the packets in transmission, any packet manipulation will cause authentication failure. In this chapter, we assume a more flexible model where a proxy, between a sender and a receiver, is able to make transcoding operations over a stream. We describe a flexible stream authentication framework that allows the so called packet independent stream authentication schemes to make transcoding operations on the packets and commit the changes, which are not applicable n packet-based stream authentication schemes. Such a stream authentication scheme based on the layered structure of a stream is elaborated in details w.r.t., the encoding, packing, amortizing, and verifying methods. The security and performance analysis show that the packet independent stream authentication schemes achieve higher authentication rate with less overhead per packet, as compared with that of packet based schemes.