Please check if you considered all CAD Geometry from your part or ipart in the FEM File. If you generate a new FEM, you can select the Geometry to use in the "New Fem" Dialog.
Typically "All Visible" is the default, please check if the correct selection is made. You can also select the geometry to use manually.
If the geometry is correctly selected the Update Polygon Bodies might help (like Tomek explained in his post).
In an existing fem, you can Rightclick the FEM File in Simulation Navigator and select "Edit". This allows you to modify the geometry in an existing simulation setup.