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First, a caveat:

Three-dimensional computations are not simple.  We have tried to make FlexPDE as easy as possible to use, but the setup and interpretation of 3D problems relies heavily on the concepts explained in 2D applications of FlexPDE.  Please do not try to jump in here without reading the preceding 2D discussion.

Extrusion:

FlexPDE constructs a three-dimensional domain by extruding a two-dimensional domain into a third dimension.  This third dimension can be divided into layers, possibly with differing material properties and boundary conditions in each layer.  The interface surfaces which separate the layers need not be planar, but there are some restrictions placed on the shapes that can be defined in this way.

The finite element model constructed by FlexPDE in three-dimensional domains is fully general.  The domain definition process is not.