Man and woman married. separated. pregnant. does father have right to baby having his last name. please help?:
Yes, if it's his baby.  They're married and although they may be separated, they're still legally bound.  The father has every right to demand that the baby be given his last name and if I were him, I would refuse to sign the birth certificate if anything else was put in.

Why assume the man left?  She didn't say that in her question.  She only said they were separated.  Maybe the mother is the one who left!