Are you measuring just the head or the head and body? In vivo or post mortem? I have used calipers to measure both head length (tip of snout to most posterior position of head at the occipital prominence). Head and body length should be done on a flat surface, snout against a fixed stop, so you can hold the body flat and measure the maximum length.

I presume you already have a protocol approved for euthanizing newborn rats?

calipers, a balance with a container to put the pup into (tare it before adding the pup!) 

practice first - plan well, (ie what you will do with the tissues after will dictate the best way to process/store them)