You mention using the sweep command. A better method would be to use the Mesh > Extrude Element command.
For this type of geometry, you may want to create Pads, etc then use the Geometry > Solid > Embed Face command. For your geometry, this worked well as shown below. The Femap Neutral file (Flange.neu) of this for your version (10.11) is part of the attached .zip file.
Using your method of surface meshing and extruding, I've split the geometry and meshed the surfaces as shown below. There is also a Femap Neutral attached of this (Flange2.neu).
Best Regards, Chip Fricke Principal Applications Engineer - Femap Product Development