You can file a Petition for Change of Entries in the Birth certificate (Change of Surname) and not the surname reflected in the ID. Under our law kasi legitimate children must use the surname of the father. Even illegitimate children may use the surname of the father provided he is recognized. Dont worry about the entries in the ID and other document po kasi once na magrant yan ng court (which im sure sure na magrant) ut will necessarily follow na machange din ang mga entries sa ID etc para magconform doon sa entries na nachange sa birthcertificate.
For legal purposes po at para hindi magulo record ng anak niyo, dapat kung ano ang nasa birth cert yun din ang nasa valid ids.
Yan Rodriguez