The following image shows the relation between elipsoid height and orthometric height, and the difference is geoid height.I think your meaning is that ,if point A is at sea and ACE30 is just referred to geoid EGM96(referred to http://corp.array.ca/nest-web/help/readers/ImportACE.html),then the geoid height of point A(also is N in the following image) must be 9.1m.Therefore,I cnnnot to mask land area based on positive data value in elevation image.
Maybe you are right.However, to achieve my goal which is to mask land area based on elevation, I want to change another method.