Actionscript 3.0, good OOP?
Looks good to me. Only thing I would say is:


The accessor methods (get / set) in Point3D are unnecessary as they don't do any processing or restrict any access. The class would be better suited to have simple, public x, y, z properties.
I don't see the purpose of the Geometry3D class. Maybe it's because I don't know much about your intentions or programming for 3d, but looks like things would be more straight-forward if indices and vertices properties were directly on Primitive3D. If it make sense to separate them off because they're processed as a pair by other parts of your program, you might also consider creating a IGeometry3D interface, which the Primitive3D class can implement. This would prevent there from being any ambiguity around ownership. (Not sure if I'm describing my thoughts, clearly.) 


I don't think getters and setters are bad for OOP programming. I think they're fantastic. They allow for validation of property values, pre- and post-processing when changing properties, lazy execution of calculations that aren't always necessary, and a lot of other things. Admittedly, you could do all of that with functions. But, to my thinking, an important part of programming is managing complexity and thoughtful use of accessor methods can simplify APIs, which in turn makes life easier (fewer bugs and easier to maintain).