Thermal analysis with multiple bodies

If mechanica understands that the two bodies share a surface it will assume them to be perfectly thermally connected. There is no option in 2001 to put in an interface resistance :-(.

Try the Autoassociate option under geometry in the edit menu. By changing the tolerance to which ProM associates, you can make the program assume that points that are close to eachother are one and the same point. This option is often automatically set to a value other than 0%, so it often causes problems with imported geometry without the user realising what's going on.

Thanks for the update. I don't need to model the interface resistance, but I do need Mechanica to realize that there are two different bodies made of different materials. Will it assume that if they are in contact when imported?

It should make that assumption. All you need to do is select each volume and assign the materials you want to them.