We got married in Manila. Then my spouse just left for Portugal and never heard of for the last 14 years. We tried to write to the Portuguese Embassy but they never replied. Does anyone know the procedure to file for separation/nullify of marriage? Thanks.

It doesn't matter where you got married.. you file in the country you are a resident of right now.

You file for divorce giving abandonment as grounds. The court will require that you try to find him to serve him notice. But there are alternatives. If you satisfy the court then you get a divorce by default.