you can as there are adapters for some of the common cabinets (Pacs, Galaga, Konami, Sega 16, etc.) and they can be made for virtually any cabinet with the correct voltages. the adapters mean you can avoid hacking a harness.
but if you're starting with an empty cabinet it's probably easier to buy a complete JAMMA harness and wire from there. they start at around $10 (though a lot of people dislike the cheap versions) and are pretty simple to install. don't forget though that with most games there are two harnesses: the AC power (to the transformer) and the DC low-voltage (from the transformer to the PCB.)
Bob Roberts has a great tutorial about how to wire this all up.