Can a new born baby be born with a hole in the top of his skull?

Skull abnormality. Yes, it is possible. The neonaologist should consult with a neurosurgeon on proper treatment.
What do you mean ? The soft spot is a normal feature in most newborns that represents where growth plates of the skull come together over the forehead. It can be very small or the width of a baseball. Occasionally a baby is born where a spot in the skin is an open wound called "cutis aplasia".