Do you mean you created vertices with the Add Vertex tool, connected them into faces with the Add Face tool, selected them with the Select Face tool, and then extruded with the Mesh Extrude tool? Or perhaps you created the faces directly with the Add face tool. It doesn't really matter, I just wanted to get the terminolgy straight about which tool is which.
If you want to extract a face, if it is a double-sided face (i.e. actually two faces facing in opposite directions) be sure when you select the face you wish to extrude, you have the "Ignore Back Faces" option selected. Otherwise JTEdit gets confused by the bace face. If you wish to make a solid out of the face (i.e. have a back-facing bottom), create the polygon with the "Double Sided" option selected. The Extract tool has a "Delete Extrusion Remainder" option for leaving in place the original face, but if it was a single-sided, forward facing face to begin with, it will stay that way, leaving your solid with a back face on the bottom, which is not generally what you want.
One problem I did encounter is that the direction the new faces on the side will face is dependent on the direction you extrude in, so they may come up back facing. I have to think about how to deal with this, because in some cases, that is what you want. You can work around this by using the Flip Faces tool afterwards. The other problem I encountered is that JTEdit should be able to handle the case of extruding double-sided faces. I'll address these issues shortly. (I'm currently out of town, so I can't do much now without my development environment.)
-John
John Thompson
http://www.jtgame.com/jtedit