I know I've seen this question asked here before, but I forgot what the awnser was, so... Why are my costom made 3dos appearing as little boxes in game?

There are a number of reasons why.
1) To many surfaces on the mesh. JK can only read 300.
2) JK can't find a mat the it needs for the 3do.
3) I've noticed that if my 3do looks appears as the box, and I import it and save it with the CMP that the level is, as well as change the CMP section in the item editor then my 3do appears.
4) Sometimes when none of that works I'll remake the 3do exactly the same and it will suddenly work. Why? I don't know, but thats a last resort.
5) Make sure you made a template for it. I'm not actually sure whether it will appear in any form without the template but I thought i'd add it, just in case.
I think I've covered everything...anybody else got any ideas?

Well, my "custom" made 3do's in this case are actually just grans and greedos with no weapons. So there can't be too many surfaces on any mesh, because I didn't add anything. All the mats are there for the 3dos too.
My level uses dflt.cmp, so they both already have the same cmp.
There was no actual "making" these 3do, I just opened them up innote pad and edited it that way. But I will keep this option as a last resort anyway.
I'm pretty sure my problem lies in the template. But I'm not really sure.

You say JK can't usemore than 300 surfaces? How about MotS? I've makeing a speeder bike 3do and it has more surfaces than 300. Is this a problem?

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I live up to my name.

Is it in a 3do folder?

Yes, it's in a 3do folder. I tried to remake the template, but it still didn't work.

MotS has the 300 surface limit too, but it's 300 surface PER MESH. Just divide up all the sectors into different layers in JED, it will multimesh it. 3dos also cannot have more than a certain number of texture verticies in one mesh, I presume 300. That's something most people don't know.