You can do this one of two ways, lay the baby on it's back as if you are changing a diaper, holding the legs up, or placing the infant across an adult's lap belly down, while the head is being supported.
To take a rectal temperature of an infant, either place the infant on his stomach on a flat surface or across your lap or place him on his back with his legs bent toward his chest. Always keep one hand on him at all times.
The baby should be on his or her tummy. You put your hand over their butt, and stick the thermometer between your fingers to hold it inside of the rectum.