The amusing part of the word prefix is that it has its own prefix. That just makes it delightful. But enough about that. I’m sure I’ll get around to its etymology one of these days. This is for the actual etymology of some prefixes.
Prefixes influence the meaning of words, and they tend to do it in the same way. For example, let’s look at a common prefix for two, bi. It shouldn’t surprise anyone that it’s Latin (i.e. Classical Latin) in origin (the same word, even). That bi- stems from the Old Latin dvi-, which is less strange if you know that in Old Latin, the v was used like a w, and dvi- would be pronounced more like dwi-. As for why d switched to b, I haven’t found a specific source on it, but I do know that Old Latin was in large part taken from the Etruscan language, and they did not have a letter b at all. The Old Latin B came from the Greeks and was probably applied to their dwi to become bi. Why? I don’t know. They liked the way it sounded, I guess. And for the record, dwi goes back even further, to the old Proto-Indo-European dwo-, which of course, meant two. But the point is, when you bi is in front of a word, it always indicates two. Sometimes, it is a slightly different variation—biannual means twice a year, bicycle means two wheels, bisexual means dual sexed—but it’s always two.
Maybe something more complex would illustrate it better. Like com-. See what I did there? See it? Okay, I’m getting entirely too pleased with myself. Back to com, and it’s children with similar meanings, con-, and co-. There is also, col-(as in colleague), and cor-(as in correlation), but they only appear in front of l and r, respectively. Like the others, they mean together or with.
Let me use complex to explain that better. The word is from the Classical Latin complexus (surrounding, encompassing), the past participle of complecti, to encircle or embrace. Plecti comes from plectere, to weave, making complecti to weave or twine together, which is a lot like embrace (when you embrace something, you wrap your arms around it…well, a lot of words seem to represent what they seem like). The point is, in literal terms, it goes from weave to weave together. This is what the com- family of prefixes does for their words.
Oh, and because I’m sure you’re curious: com- appears when the root word begins with b, l, m, p, or r. Con- appears in front of c, d, j, n, q, s, t, v. Finally, co- appears before the vowels and letters that can sound like vowels, like h, as well as gn, which is in a lot of words, like cognizance. There are also co- words that were once two parts (costar used to be co-star; codependent used to be co-dependent) but lost the dash along the way.
The Online Etymology Dictionary
Latin Pronunciation Demystified by Michael A. Covington of the University of Georgia.