As frustrating as it seems, your doctor is likely correct. 3 1/2 months is still very young and the skull is still very flexible. As she grows and becomes more mobile her skull shape will normalize. If you are truly concerned that there may be a problem, ask you doctor to order an xray to rule out any abnormalities. This is really not necessary if the baby is thriving and growing and otherwise meeting developmental milestones.
Hang in there...it's just easier to see her skull shape without hair to cover it up. If all of us went around bald, we have a much better sense of humor about life because head shapes are very weird!! This will all be forgotten by her first birthday!!
C