While it might seem like "manner" itself is the suffix, it's actually the whole word. The "-er" suffix is often used to create nouns that describe someone or something that does something. For example:
* teach + -er = teacher (someone who teaches)
* walk + -er = walker (someone who walks)
In the case of "manner," the word likely comes from an older form (possibly related to "man" or "hand"), and "-er" was added to indicate the way something is done.