As the etymology of the word suggests, a manuscript is something written (Latin scriptus) by hand (manus). Before the invention of printing around 1450, all works were circulated in manuscript (often abbreviated MS in the singular and MSS in the plural). Even after the invention of printing, many MSS continued to circulate.

An autograph manuscript is one written in the hand of the author (as opposed to a copyist or secretary).

Sometimes the term is used more loosely: when publishers refer to the manuscripts of twentieth-century authors, they usually mean typescripts, i.e., the author's typed draft from which the typesetters worked. In this sense, a manuscript can be the form of any work not yet printed. In the age of desktop publishing, that distinction will get ever more difficult to preserve.

From the Guide to Literary Terms by Jack Lynch.
Please send comments to Jack Lynch.
Note: This guide is still in the early stages of development.
Three question marks mean I have to write more on the subject. Bear with me.