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I have my mesh under dummyroot, with a duplicated, lower-res version for the collision. How do I proceed from that into exporting it so I can use it? The mod tool documentation is very basic and only really goes into what works with the old Pandemic addon and I can't find what I'm looking for on the FAQ/Everything you need thread.

I would like to know which version of Softimage ModTool you are currently using. I use Version 7.5 and installed Ande's ZeTools. They work perfectly and do the exact same as using pandemic's xsiAddon to export objects and animations. You'll need to branch DummyRoot and then go to ZeTools tab and press "export msh". You just still need to choose your destination folder and then you're done with this.

I got that bit handled but I don't know what visibility options I need for collision and LOD parts. I have Mod Tools 7.5

Lowrez and Collisions can be hidden. The game will still read and accept it. I often hide _lowrez(s) and collisions because they mostly confuse me when editing the general object.

I know im late here but when i export model i click on the DummyRoot with my middle mouse button.Then the whole tree will be selected like that.Before that hide with H butoon the collision and lowrez.Then click ZeTools/export.Choose where to export the model,give him name and click export.Thats all.Atleast thats what im doing.

If you're making a prop or building you don't want to hide the lowrez mesh because it will be difficult to accurately place the object in ZE since it displays the lowrez geometry. Also, with ZETools you don't need to branch select the root node, you only need to left click select the root node and ZETools will collect all child data automatically while exporting.