Can you rent a car with a manual transmission and if so where?

There is, but you'd probably have to go to Europe or Asia or Africa to find them. In the US, none of the major rental agencies will have any (nor do they rent out diesel vehicles, either), simply because there's too much liability. Manual transmissions are not the norm here, and thus, a very small percentage of people learn how to drive them, and an even smaller percentage learn how to drive them properly, at that. Since the agency has no way of actually knowing whether the person renting the car actually does know how to drive one, it's much less of a gamble to just have an automatic transmission. Otherwise, they'd end up with a whole lot spent in repair bills from people who wear down the friction disc face, people who destroy the synchronizer gears thinking they don't have to use the clutch when they shift, etc.