Hmmm... maybe the ignore option is the trick? Or does that just not select polys at the back of the model?
If you want to take a stab at Blender I think I have a solution. Forgive me, I'm going to outline the steps in a long post. It's not much work I'm just breaking it down so it's easy to follow.
This process is based on Blender 2.45 (it's what's in front of me without rebooting and switching OSs) but should work at least up to version 2.49
1. Start Blender
2. At the top click on File > Load Factory Settings > (answer ok to erase all). This step is just to make sure we are looking at the same thing and there isn't a custom setup to worry about.
3. Tap the TAB key until the mode is Object Mode. There should be a little view box about midway down the screen that will display the current mode.
4. RIGHT CLICK on the cube in the middle of the grid. It should highlight purple/pink if it isn't already.
5. Press X to delete the object
6. Click File > Import > Direct X (or whatever file format is available that you want to change. For our purposes we'll stick with Direct X) Import your object.
Press SHIFT+C and then press C. This will center everything in the view so it's all visible.
7. Right click on the object. If an object is made up of multiple limbs, they will all load as individual objects. RIGHT CLICKING selects an individual mesh/object.
8. Press F7 to open the object control panel. At the bottom of the screen there should be a panel with the heading
Draw. Within this panel there should be a series of buttons under the heading
Drawtype. Click on the button labeled
Solid. If you weren't already, you should be in solid mode. This is the mode that's going to allow us to separate the inside and the outside polygons.
9. Tap TAB to toggle to Edit mode.
10. Press CTRL+TAB+3 to enter polygon mode
11. Tap 'A' key until NONE of the faces are selected.
12. There is a menu bar dividing the grid on which the cube is draw and the panel area where you selected solid. This menu bar has a control on the FAR LEFT that looks like a little 3d cube. It should be next to a button with a triangle on it that is depressed. The triangle button is the control to be in face mode which we used shortcuts to activate.
Anyway, this cube button will control whether we can select all of the faces, or just the visible ones. We want to press this button (click on it) to select just the visible ones. If you hover the mouse over it, it reads
Limit Selection to Visible
13. We're almost there! Move the mouse onto the grid. Press the 'B' key and a dotted plus will appear. This is Box Select mode. Hold the LEFT MOUSE BUTTON and drag a box around the object. All of the visible faces should highlight.
Now, some of the faces on the outside might have been out of the camera view. With the mouse in the grid screen, hold the LEFT and RIGHT buttons simultaneously and move the mouse around to rotate the camera view. If you see any faces that are not selected, release the mouse buttons, press B, abd select the object again.
Once you are sure all of the outside faces are selected, press '7' on the numerical key pad to return to the default view. If you need to, you can center the screen as we did in the beginning - but you don't have to.
14. On the middle menu bar, click on Select > Inverse . This will highlight all of the hidden polygons.
15. Press the 'X' key and click on Faces to erase the hidden faces.
16. You are done! Toggle to Object mode (TAB key) and right click to select any other objects/meshes that were imported and run through the same selection/deletion stuff.
Likely, there's going to be some missed polygons, or a few doubled polygons. Handle those on an exception basis. Once you get the short cut keys down, this entire process only takes a couple of minutes at most to do in Blender. Once you've removed the doubles and exported your model, you can tweak it in an app you're more comfortable with.
There are many threads on exporting an X file from Blender so I won't get into that.
Enjoy your day.